diff --git a/docs/Changelog.rst b/docs/Changelog.rst index 967c3f0a..5873e559 100644 --- a/docs/Changelog.rst +++ b/docs/Changelog.rst @@ -5,6 +5,11 @@ Changelog for EasyBuild documentation (for EasyBuild release notes, see :ref:`release_notes`) +* **release 20200414.01** (`Apr 14th 2020`): + + * document new EasyBuild locking mechanism (see :ref:`locks`) + * document support for creating index files (see :ref:`easyconfigs_index`) + * update release notes for EasyBuild v4.2.0 (see :ref:`release_notes_eb420`) * **release 20200316.01** (`Mar 16th 2020`): update release notes for EasyBuild v4.1.2 (see :ref:`release_notes_eb412`) * **release 20200116.01** (`Jan 16th 2020`): update release notes for EasyBuild v4.1.1 (see :ref:`release_notes_eb411`) * **release 20191204.01** (`Dec 4th 2019`): update release notes for EasyBuild v4.1.0 (see :ref:`release_notes_eb410`) diff --git a/docs/Easyconfigs_index.rst b/docs/Easyconfigs_index.rst new file mode 100644 index 00000000..333c9dd0 --- /dev/null +++ b/docs/Easyconfigs_index.rst @@ -0,0 +1,175 @@ +.. _easyconfigs_index: + +Using an index to speed up searching for easyconfigs +==================================================== + +EasyBuild often needs to search for :ref:`easyconfig_files` (or accompanying files like patches), +either based on command line arguments (like the name of an easyconfig file) +or options to the ``eb`` command (like ``--search``, see :ref:`searching_for_easyconfigs`), +or to resolve dependencies for a particular easyconfig file that was parsed already. + +Searching for easyconfig files or patches may take a while, since it can potentially involve weeding through +thousands of files, which may be located on a shared filesystem (where metadata-intensive operations like +file searching can be rather slow). + +If EasyBuild turns out to be sluggish when searching for easyconfig files in your setup, +using an *index* file could make a big difference. + +.. note:: Support for index files was implemented in EasyBuild version 4.2.0 . + + +.. contents:: + :depth: 3 + :backlinks: none + + +.. _easyconfigs_index_create: + +Creating an index (``--create-index``) +-------------------------------------- + +``eb --create-index`` can be used to create an index file for a particular directory +that holds a (large) set of easyconfig files. + +The index file (a hidden file named ``.eb-path-index``) will be created in the specified directory. +It will contain a list of (relative) paths for all files in that directory, +along with some metadata: the time at which the index file was created +and a timestamp that indicates how long the index is considered to be valid (see :ref:`easyconfigs_index_max_age`). + +.. note:: + Make sure to create an index for the correct path. + + The search for easyconfig files performed by EasyBuild will *not* recurse into subdirectories of the locations + it considers (see :ref:`robot_search_path`), other than those with a name matching the + software for which it is trying to find an easyconfig file (like ``t/TensorFlow/`` when searching for an + easyconfig file for ``TensorFlow``). + + Hence, if the directory housing your easyconfig files has an ``easybuild/easyconfigs`` subdirectory + (for example, a working copy of the ``easybuild-easyconfigs`` repository), create the index *in* that + subdirectory, rather than in the higher-level directory. + + +.. _easyconfigs_index_create_example: + +Example of creating an index +~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +.. code:: + + $ eb --create-index $HOME/easybuild-easyconfigs/easybuild/easyconfigs + == temporary log file in case of crash /tmp/eb-tUu6_w/easybuild-SKBnVO.log + Creating index for /home/example/easybuild-easyconfigs/easybuild/easyconfigs... + == found valid index for /home/example/easybuild-easyconfigs/easybuild/easyconfigs, so using it... + Index created at /home/example/easybuild-easyconfigs/easybuild/easyconfigs/.eb-path-index (738 files) + + $ head -n 5 $HOME/easybuild-easyconfigs/easybuild/easyconfigs/.eb-path-index + # created at: 2020-04-13 14:19:57.008981 + # valid until: 2020-04-20 14:19:57.008981 + a/Arrow/Arrow-0.16.0-intel-2019b-Python-3.7.4.eb + b/Boost/Boost-1.71.0-gompi-2019b.eb + b/bokeh/bokeh-1.4.0-foss-2019b-Python-3.7.4.eb + + +.. note:: + The "``found valid index ...``" message being printed occurs because EasyBuild tries to load the index file + right after creating it, as a sanity check. + + +.. _easyconfigs_index_update: + +Updating an existing index (``--create-index --force``) +------------------------------------------------------- + +To update an existing index, you can use ``--create-index --force``. + +Without using ``--force``, EasyBuild will refuse to overwrite the existing index file:: + + $ eb --create-index $HOME/easybuild-easyconfigs/easybuild/easyconfigs + == temporary log file in case of crash /tmp/eb-tUu6_w/easybuild-SKBnVO.log + Creating index for /home/example/easybuild-easyconfigs/easybuild/easyconfigs... + ERROR: File exists, not overwriting it without --force: /home/example/easybuild-easyconfigs/easybuild/easyconfigs/.eb-path-index + + +.. _easyconfigs_index_use: + +Using index files +----------------- + +EasyBuild will automatically pick up and use any index file that it runs into while searching for +easyconfig files or patches. If an index file is found, it will be preferred over walking through +the directory tree to check for the target file, which is likely to significantly speed up the search operation. + +When a (valid) index file is found for a particular path, a message will be printed mentioning "``found valid index +for...``":: + + $ eb --search TensorFlow-2.1.0-foss-2019b + == found valid index for /home/example/easybuild-easyconfigs/easybuild/easyconfigs, so using it... + * /home/example/easybuild-easyconfigs/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.1.0-foss-2019b-Python-3.7.4.eb + + +.. _easyconfigs_index_ignore: + +Ignoring indices (``--ignore-index``) +------------------------------------- + +One potential issue with having an index in place is that it may get outdated: +new files may have been added to the directory since the index was created or last updated. + +If updating the indexes is not an option (see :ref:`easyconfigs_index_update`), +you can instruct EasyBuild to ignore any existing indices using the ``--ignore-index`` +configuration option. + +The only downside of this option is that searching for easyconfig files may be significantly slower. +Any existing index files are left untouched (they will *not* be updated or removed). + + +.. _easyconfigs_index_max_age: + +Controlling how long the index is valid (``--index-max-age``) +------------------------------------------------------------- + +When creating an index file, you can specify how long the index should be considered valid. + +Using the ``--index-max-age`` configuration option, you can specify how long after the creation time +the index remains valid (in seconds). + +By default, EasyBuild will consider index files to remain valid for 1 week (7 * 24 * 60 * 60 = 604,800 seconds). + +To create an index that *always* remains valid (never expires), use zero (``0``) as value for ``--index-max-age``:: + + $ eb --create-index --index-max-age=0 $HOME/easybuild-easyconfigs/easybuild/easyconfigs + + $ head -n 2 $HOME/easybuild-easyconfigs/easybuild/easyconfigs/.eb-path-index + # created at: 2020-04-13 15:10:07.173191 + # valid until: 9999-12-31 23:59:59.999999 + +.. note:: Trust us here, December 31st 9999 is the end of times. Better get prepared. + + +.. _easyconfigs_index_release: + +Index included with EasyBuild releases +-------------------------------------- + +Each EasyBuild release (since EasyBuild v4.2.0) comes with an index file for the easyconfig (and patch) files +that are included with that release. + +Hence, you only need to use ``--create-index`` to create/update the index file for any additional directories +with easyconfig files you may have on the side (and only if searching those easyconfig files is rather slow). + + +.. _easyconfigs_index_should_use: + +Should I create an index? +------------------------- + +Whether or not you should create an index file for your directories housing additional easyconfig files depends on a number of factors, including: + +* how often files are added and/or removed in those directories, since files listed in the index are assumed to be there and any files not included in the index will be overlooked by EasyBuild when it's searching for files; + +* the filesystem on which those directories are located, since an index file will only make a significant difference on filesystems where metadata-intensive operations are relatively slow; + +* how many files there are in those directories, since performance benefits will only be apparent if the number if files is sufficiently large; + +.. note:: Keep in mind that creating an index implies also updating it frequently, + to ensure that EasyBuild will take all available files in account. diff --git a/docs/Including_additional_Python_modules.rst b/docs/Including_additional_Python_modules.rst index 67f172e7..7deedb46 100644 --- a/docs/Including_additional_Python_modules.rst +++ b/docs/Including_additional_Python_modules.rst @@ -85,6 +85,9 @@ Generic easyblocks are expected to be located in a directory named ``generic``. To verify that the easyblocks you included are indeed being picked up, ``--list-easyblocks=detailed`` can be used (see also :ref:`list_easyblocks`). +Since EasyBuild 4.2.0, easyblocks from a pull request on GitHub can also be included, +using ``--include-easyblocks-from-pr`` (see :ref:`github_include_easyblocks_from_pr`). + Example ~~~~~~~ diff --git a/docs/Integration_with_GitHub.rst b/docs/Integration_with_GitHub.rst index 81eb29af..d9c7770c 100644 --- a/docs/Integration_with_GitHub.rst +++ b/docs/Integration_with_GitHub.rst @@ -353,6 +353,38 @@ in that same pull request for netCDF, WRF, ...:: Again, note that locally available easyconfigs that are required to resolve dependencies are being picked up as needed. +.. _github_include_easyblocks_from_pr: + +Using easyblocks from pull requests (``--include-easyblocks-from-pr``) +---------------------------------------------------- + +*(supported since EasyBuild v4.2.0)* + +Via the ``--include-easyblocks-from-pr`` command line option, easyblocks that are added or +modified by a particular pull request to the `easybuild-easyblocks GitHub repository +`_ can be used (regardless of whether the pull request is merged +or not). + +This can be useful to employ easyblocks that are not available yet in the active EasyBuild installation, +or to test new contributions by combining ``--include-easyblocks-from-pr`` with ``--from-pr`` and ``--upload-test-report`` +(see :ref:`github_upload_test_report`). + +When ``--include-easyblocks-from-pr`` is used, EasyBuild will download all modified easyblocks to a temporary +directory before processing them. Just like with ``--include-easyblocks`` (see :ref:`include_easyblocks`), +the easyblocks that are included are preferred over the ones included in the EasyBuild installation. + +For example, to use the LAMMPS easyblock contributed via `easyblocks pull request #1964 +`_ together with the LAMMPS v7Aug2019 easyconfigs contributed via +`easyconfigs pull request #9884 `_:: + + $ eb --from-pr 9884 --include-easyblocks--from-pr 1964 --list-easyblocks=detailed + == temporary log file in case of crash /tmp/eb-Eq2zsJ/easybuild-1AaWf8.log + EasyBlock (easybuild.framework.easyblock) + ... + | | |-- EB_LAMMPS (easybuild.easyblocks.lammps @ /tmp/included-easyblocks-rD2HEQ/easybuild/easyblocks/lammps.py) + ... + + .. _github_upload_test_report: Uploading test reports (``--upload-test-report``) diff --git a/docs/Locks.rst b/docs/Locks.rst new file mode 100644 index 00000000..f2a92f35 --- /dev/null +++ b/docs/Locks.rst @@ -0,0 +1,102 @@ +.. _locks: + +Locks to prevent duplicate installations running at the same time +================================================================= + +Easybuild creates a lock before starting the installation of an easyconfig file, +to avoid a collision between multiple installations running at the same time. + +If an EasyBuild session tries to install an easyconfig file when a lock for that installation already exists, +it will be automatically aborted with an error like "``Lock ... already exists, aborting!``". + +.. note:: Locking of installations was implemented in EasyBuild version 4.2.0 . + + +.. contents:: + :depth: 3 + :backlinks: none + +.. _locks_implementation: + +Locking implementation details +------------------------------ + +Easybuild will create a lock when starting an installation if no corresponding lock exists yet, +regardless of whether the installation was requested explicitly or is performed to resolve a dependency. + +The name of the lock corresponds to the *full* path of the installation directory, with slashes (``/``) and +dashes (``-``) replaced by underscores (``_``), and with an additional ``.lock`` added at the end. + +Locks are created in the :ref:`locks_dir`. + +The lock created by EasyBuild is an empty directory (rather than a file), +because that can be created more atomically on modern filesystems. + +For example, if ``OpenFOAM-7-foss-2019b.eb`` is being installed to ``/apps/easybuild/software``, +an empty directory that serves as a lock for this installation will be created at +``/apps/easybuild/software/.locks/_apps_easybuild_software_OpenFOAM_7_foss_2019b.lock`` +(assuming the default :ref:`locks_dir` is used). + +A lock is automatically removed by Easybuild when the installation ends, regardless of whether the installation +was successful or not. Therefore, new installations of the same easyconfig will be aborted in case of: + +* another installation for the same easyconfig is in progress; +* a previous installation of the same easyconfig was abruptly interrupted; + + +.. _locks_removing: + +Removing locks +-------------- + +If a previous installation was abruptly interrupted and a lock was left in place, +it can be easily removed using the ``rmdir`` command (since the lock is actually an empty directory). + + +.. _locks_configuration_options: + +Configuration options related to installation locks +--------------------------------------------------- + +The behaviour of the locking mechanism in Easybuild can be tuned with the following configuration options: + +.. _locks_ignore: + +Ignoring locks (``--ignore-locks``) +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +Using the ``--ignore-locks`` configuration option, you can instruct EasyBuild to ignore any existing locks. +Locks that exist are left untouched, even if the installation completes successfully. + +**Use this with caution, since installations may be (partially) overwritten if another EasyBuild session is also +performing those installations!** + + +.. _locks_wait: + +Waiting for locks to be removed (``--wait-on-lock``) +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +Using the ``--wait-on-lock`` configuration option, you can change how EasyBuild deals with existing locks, +by specifying how frequently EasyBuild should check whether an existing lock was removed. By specifying a non-zero value ``S``, +you can indicate how many seconds EasyBuild should wait before checking again whether the lock is still in place. + +.. note:: EasyBuild will wait indefinitely for an existing lock to be removed if ``--wait-on-lock`` is set to a non-zero value... + + If the lock is never removed, the EasyBuild session will never terminate; it will keep checking every ``S`` seconds whether the lock is still in place. + +By default, EasyBuild will *abort* the installation with an error like "``Lock ... already exists, aborting!``" +if a corresponding lock already exists, which is equivalent to setting ``--wait-on-lock`` to zero (``0``), +implying that no waiting should be done at all. + + +.. _locks_dir: + +Locks directory +--------------- + +If desired, an alternate location where locks should be created and checked for can be specified via the ``--locks-dir`` configuration option. + +.. note:: Keep in mind that a path on a *shared* filesystem should be used, to ensure that active EasyBuild sessions running on different systems use the same locks directory. + +By default, locks are created in a hidden subdirectory ``.locks`` in the top-level ``software`` installation directory; that is, the ``software`` subdirectory of the ``installpath`` configuration setting of the active EasyBuild session. diff --git a/docs/Release_notes.rst b/docs/Release_notes.rst index bd584692..b1decf3a 100644 --- a/docs/Release_notes.rst +++ b/docs/Release_notes.rst @@ -3,12 +3,261 @@ EasyBuild release notes ======================= -The latest version of EasyBuild provides support for building and installing **1,798** different software packages, -including 31 different (compiler) toolchains. It contains 212 software-specific easyblocks and 36 generic easyblocks, -alongside 8,964 easyconfig files. +The latest version of EasyBuild provides support for building and installing **1,912** different software packages, +including 31 different (compiler) toolchains. It contains 219 software-specific easyblocks and 36 generic easyblocks, +alongside 9,462 easyconfig files. .. note:: See also the :ref:`concise overview of major changes in EasyBuild v4.0 `. +.. _release_notes_eb420: + +EasyBuild v4.2.0 (April 14th 2020) +---------------------------------- + +feature release + +**framework** + +* add support for ``--try-update-deps`` (experimental feature), to upgrade dependencies based on available easyconfigs (`#2599 `_) + +* adding locking to prevent two parallel builds of the same installation directory (`#3009 `_) + + * for more information, see https://easybuild.readthedocs.io/en/latest/Locks.html + +* significantly speed up ``-D/--dry-run`` by avoiding useless '``module show``' (`#3203 `_) + +* add support for creating an index & using it when searching for easyconfigs (`#3210 `_) + + * for more information, see https://easybuild.readthedocs.io/en/latest/Easyconfigs_index.html + +* additional GitHub integration features: + + * add support for targeting easyblocks and framework repositories in ``--new-pr`` (`#1876 `_, `#3189 `_) + * add support for ``--include-easyblocks-from-pr`` (`#3206 `_) + * for more information, https://easybuild.readthedocs.io/en/latest/Integration_with_GitHub.html + +* various other enhancements, including: + + * add a contrib/hooks dir with some examples of hooks used (`#2777 `_) + * also mention working directory + input passed via stdin (if any) in trace output of ``run_cmd`` (`#3168 `_) + * probe external modules for missing metadata that is not provided via extermal module metadata file (`#3174 `_) + * also update ``$CMAKE_PREFIX_PATH`` and ``$CMAKE_LIBRARY_PATH`` in generated module file (`#3176 `_) + * optionally call ``log.warning`` in ``print_warning`` (`#3195 `_) + * add an option to ``git_config`` to retain the ``.git`` directory (`#3197 `_) + * allow use of ``SYSTEM`` as ``--try-toolchain`` option (`#3213 `_) + * mention CPU arch name in comment for uploaded test report, if it's known by ``archspec`` (`#3227 `_) + * make ``--merge-pr`` take into account ``--pr-target-branch`` (`#3236 `_) + * make ``--check-contrib`` print a warning when ``None`` is used for checksums (`#3244 `_) + * update ``install-EasyBuild-develop.sh`` script and create script for 2020a merge sprint (`#3245 `_) + * add template for ``mpi_cmd_prefix`` (`#3264 `_) + * update ``copy_dir`` to include option to merge directories (`#3270 `_) + * support template name for CUDA version (`#3274 `_) + +* various bug fixes, including: + + * use correct module for ``errors_found_in_log`` (`#3119 `_) + * fix ``EasyConfig.update`` code to handle both strings and lists as input (`#3170 `_) + * fix removing temporary branch on ``--check-github`` (`#3182 `_) + * fix shebang even if first line doesn't start with '``#!``' (`#3183 `_) + * make bootstrap script work with Python 3 (`#3186 `_) + * read patch files as bytestring to avoid ``UnicodeDecodeError`` for patches that include funky characters (`#3191 `_) + * fix online check in ``--check-github``: try repeatedly and with different URLs to cater for HTTP issues (`#3194 `_) + * don't crash when GitPython is not installed when using Python 3 (`#3198 `_) + * fix ``os_name_map`` for RHEL8 (`#3201 `_) + * don't add shebang to binary files (`#3208 `_) + * use ``checkout@v2`` in GitHub Actions to fix broken re-triggered tests (`#3219 `_) + * don't filter out ``None`` values in to_checksums, leave them in place (`#3225 `_) + * fix defining of ``$MPI_INC_*`` and ``$MPI_LIB_*`` environment variables for impi version 2019 and later (`#3229 `_) + * use correct target account/repo when creating test report & posting comment in PR (`#3234 `_) + * reorganize ``EasyBlock.extensions_step`` to ensure correct filtering of extensions (`#3235 `_) + * also support ``%(installdir)s`` and ``%(builddir)s`` templates for extensions (`#3237 `_) + * unset ``$GITHUB_TOKEN`` in Travis after installing token, to avoid failing ``test_from_pr_token_log`` (`#3252 `_) + * fix reporting when skipping extensions (`#3254 `_) + * avoid API rate limit errors on online check in ``--check-github`` (`#3257 `_) + * show easyconfig filenames for parallel build (`#3258 `_) + * make ``EasyConfig.dump`` aware of toolchain hierarchy, to avoid hardcoded subtoolchains in dependencies easyconfig parameters (`#3261 `_) + * fix use of ``--copy-ec`` with a single argument, assume copy to current working directory (`#3262 `_) + * fix posting of comment in PR with ``--upload-test-report`` (`#3272 `_) + * take into account dependencies marked as external modules when composing template values like ``%(pyver)s`` (`#3273 `_) + +* other changes: + + * increase timeout & use ``api.github.com`` for connectivity check in ``check_github`` (`#3192 `_) + * restore ``flake8`` default ignores (`#3193 `_) + * enable tracking of test suite coverage using coveralls (`#3204 `_) + * make tests use ``easybuilders/testrepository`` rather than ``hpcugent/testrepository`` after it was moved (`#3238 `_) + * improve raised error in ``remove_dir`` and deprecate ``rmtree2`` (`#3228 `_) + +**easyblocks** + +* 7 new software-specific easyblocks: + + * BerkeleyGW (`#1951 `_), CMake (`#1936 `_), ELSI (`#1883 `_), LAMMPS (`#1964 `_, `#1975 `_, `#1978 `_, `#1982 `_, `#1997 `_), libdrm (`#1983 `_), Mesa (`#1892 `_, `#2006 `_), SEPP (`#1998 `_) + +* minor enhancements, including: + + * make ParMETIS easyblock compatible with custom ``configopts`` (`#1774 `_) + * update Trinity easyblock for v2.9.0 (`#1906 `_) + * disable ROCM and Android workspace explicitly in TensorFlow easyblock (`#1944 `_) + * update QuantumESPRESSO easyblock for version 6.5 (`#1947 `_) + * update Siesta easyblock to support MaX-1.0 release (`#1954 `_) + * update Ferret easyblock for versions >= 7.5.0 (`#1956 `_) + * update XCrySDen easyblock to support Togl dependency (`#1959 `_) + * pass value for ``TARGET`` specified in ``buildopts`` to ``testopts`` and ``installopts`` in OpenBLAS easyblock (`#1960 `_) + * fix netCDF(-Fortran) support in Siesta easyblock (`#1967 `_, 1971) + * add ``NCDF_PARALLEL`` and METIS support to Siesta easyblock (`#1973 `_) + * add support for ``use_pip_extras`` custom easyconfig parameter in ``PythonPackage`` easyblock (`#1980 `_) + * update Open Babel easyblock for version 3.0.0 (`#1992 `_) + * allow differing names for TensorFlow wheel (`#1995 `_) + * make MATLAB runtime available from MATLAB (`#2008 `_) + +* various bug fixes, including: + + * fix linking of Hypre to external BLAS/LAPACK + support building (only) static/shared library (`#1885 `_) + * fix MPI-CXX dependency of PETSc (`#1917 `_) + * limit amount of parallelism in TensorFlow easyblock (`#1934 `_) + * support GCCcore and gcc4.8 (if that dir exists) in function ``get_tbb_gccprefix`` in tbb easyblock (`#1943 `_) + * restore default ``flake8`` warnings (`#1950 `_) + * remove tests from ``build_step`` and raise error on failed tests in OpenBLAS easyblock (`#1952 `_, `#1955 `_, `#1962 `_) + * add optional ``runtest`` to the catch for ``FATAL ERRORS`` to OpenBLAS easyblock (`#1958 `_) + * ensure right '``python``' command is used to determine Python lib dir when system Python is used with PythonBundle easyblock (`#1961 `_) + * make sure ``lib/python*/lib-dynload`` exists in Python installation (`#1966 `_) + * in version 6.0 of TensorRT, ``libnvinfer.a`` is renamed ``libnvinfer_static.a`` (`#1970 `_) + * handle ``configopts`` without configure args in CMake easyblock (`#1974 `_) + * use ``checkout@v2`` in GitHub Actions to fix broken re-triggered tests (`#1976 `_) + * don't insist that pylibdir always exists in OpenCV easyblock (`#1977 `_) + * also set ``$TRINITY_HOME`` environment variable in Trinity easyblock (`#1979 `_) + * fix sanity check for OpenFOAM-Extend >= 4.1 (`#1981 `_) + * fix pattern matching in regex subst for ``I_MPI_ROOT`` in impi easyblock (`#1986 `_) + * use ``remove_dir`` instead of deprecated ``rmtree2`` in various easyblocks (`#1993 `_) + * fix "``AttributeError: module 'git' has no attribute 'Git'``" that may occur when using Python 3 (`#1994 `_) + * don't sanity check for ``QtWebEngine`` in Qt easyblock when building for POWER (`#2000 `_) + * fix installation of TensorFlow in some environments, by setting ``$PYTHONNOUSERSITE`` (& more) (`#2002 `_, `#2020 `_) + * make sure libxml2 is built with XZ provided as dependency (`#2005 `_) + * look for Python version directories with suffixes in ROOT easyblock (`#2010 `_) + * enable TK, FLTK and OPENGL configure options in VMD easyblock (`#2013 `_) + * update the contributing docs (`#2014 `_) + * fix numexpr easyblock to allow (correctly) installing it as extension (`#2022 `_) + +* other changes: + + * simplify various CMakeMake-based easyblocks by enhancing ``CMakeMake`` (w.r.t. ``CMAKE_BUILD_TYPE``, shared vs static libs, ``-fPIC``) (`#1929 `_) + * enable out of tree build by default in ``CMakeMake`` easyblock (`#1933 `_) + * force building Clang without CUDA when it is not found as a proper dependency (`#1968 `_) + +**easyconfigs** + +* added example easyconfig files for 114 new software packages: + + * ABRA2 (`#10272 `_), ABRicate (`#10310 `_), ADIOS (`#10036 `_), aNCI (`#9929 `_), any2fasta (`#10310 `_), apex (`#10269 `_), + archspec (`#9898 `_), ArviZ (`#10366 `_), autopep8 (`#9626 `_), BAMSurgeon (`#10330 `_), BatMeth2 (`#10323 `_), + BiG-SCAPE (`#10352 `_), BinSanity (`#10001 `_), Bonito (`#10269 `_), BSMAPz (`#10283 `_), BSseeker2 (`#10039 `_), + BUStools (`#9838 `_), Cbc (`#10052 `_), Cgl (`#10048 `_), CGmapTools (`#10288 `_), Clp (`#10033 `_), CoinUtils (`#9937 `_), + dtcwt (`#9695 `_), ELSI (`#9857 `_), EnsEMBLCoreAPI (`#8734 `_), fastq-pair (`#9894 `_), FigureGen (`#10076 `_), Fiona (`#10321 `_), + FuSeq (`#10004 `_), GenomeTools (`#9797 `_), GraphMap2 (`#10299 `_), GRASP (`#9896 `_), Groovy (`#9809 `_), gsport (`#9821 `_), + gubbins (`#9689 `_), igv-reports (`#9977 `_), inferCNV (`#9686 `_), iVar (`#10291 `_), joypy (`#10212 `_), JupyterLab (`#9752 `_), + kma (`#10259 `_), LAMMPS (`#10371 `_), lancet (`#10271 `_), libBigWig (`#10006 `_), libGridXC (`#9858 `_), libPSML (`#5859 `_), + LtrDetector (`#10343 `_), manta (`#5104 `_), medImgProc (`#10228 `_), MedPy (`#9748 `_), Mini-XML (`#10036 `_), mkl_fft (`#9887 `_), + Monocle3 (`#9825 `_), MoreRONN (`#10255 `_), motionSegmentation (`#10228 `_), NanoComp (`#10212 `_), NanoFilt (`#10212 `_), + nanoget (`#10212 `_), nanomath (`#10212 `_), NanoPlot (`#10212 `_), ngspice (`#9922 `_), ntEdit (`#9836 `_), ntHits (`#9833 `_), + occt (`#9939 `_), OCNet (`#9955 `_), OpenAI-Gym (`#10347 `_), OpenPIV (`#9959 `_), OpenPyXL (`#10115 `_), orca (`#9518 `_), + Osi (`#10361 `_), PartitionFinder (`#9983 `_), pauvre (`#10212 `_), polymake (`#9904 `_), pretty-yaml (`#10041 `_)), + PRSice (`#9988 `_), pycodestyle (`#9626 `_), pydot (`#9899 `_), pygraphviz (`#9969 `_), pylift (`#10051 `_), PyMC3 (`#10279 `_), + pyparsing (`#9983 `_), PyRe (`#10095 `_), python-weka-wrapper3 (`#9704 `_), PyTorch-Geometric (`#9995 `_), qcat (`#10244 `_), + RAxML-NG (`#9990 `_), Ray (`#10302 `_), rclone (`#7934 `_), Red (`#9856 `_), rstanarm (`#9964 `_), scikit-build (`#9762 `_), + scVelo (`#9805 `_), SECAPR (`#9721 `_), segmentation-models (`#10211 `_), SentencePiece (`#10192 `_), SEPP (`#10047 `_), + Shapely (`#10309 `_), Singular (`#10030 `_), SLATEC (`#7529 `_), spatialreg (`#9767 `_), split-seq (`#9749 `_), spoa (`#9705 `_), + SSN (`#9955 `_), STEAK (`#10337 `_), stpipeline (`#9736 `_), SVG (`#9905 `_), Togl (`#9868 `_), torchtext (`#10193 `_), + units (`#9682 `_), UQTk (`#10279 `_), WildMagic (`#10044 `_), Winnowmap (`#10005 `_), xtb (`#9993 `_), Zip (`#9972 `_) + +* added additional easyconfigs for various supported software packages, including: + + * ABySS 2.1.5, Arrow 0.16.0, BCFtools 1.10.2, BEDTools 2.29.2, BUSCO 4.0.5, BerkeleyGW 2.1.0, binutils 2.34, + CVXPY 1.0.28, CharLS 2.1.0, CheckM 1.1.2, Clang 10.0.0, CppUnit 1.15.1, canu 1.9, cutadapt 2.8, + DIAMOND 0.9.30, davix 0.7.5, ELPA 2019.11.001, FastANI 1.3, FastQC 0.11.9, Ferret 7.5.0, GATK 4.1.4.1, + GCCcore 9.3.0, GDB 9.1, GMAP-GSNAP-2019-09-12, GObject-Introspection 1.63.1, GPAW 20.1.0, GROMACS 2020, + GTDB-Tk 1.0.2, GTK+ 3.24.13, Go 1.14.1, Gradle 6.1.1, GraphicsMagick 1.3.34, Graphviz 2.42.2, Gurobi 9.0.1, + gSOAP 2.8.100, gnuplot 5.2.8, gtest 1.10.0, HDDM 0.7.5, HTSlib 1.10.2, HarfBuzz 2.6.4, Horovod 0.19.1, + Hypre 2.18.2, IGV 2.8.0, IQ-TREE 1.6.12, IRkernel 1.1, iccifort 2020.0.166, igraph 0.8.0, impi 2019.6.166, + ispc 1.12.0, Java 13(.0.2), Julia 1.4.0, Keras 2.3.1, Kraken2 2.0.8-beta, kim-api 2.1.3, LAST 1045, + LASTZ 1.04.03, LLVM 9.0.1 + 10.0.0, LMfit 0.9.14, LS-PrePost 4.7.8, likwid 5.0.1, MAFFT 7.453, + MATLAB 2019b, MMseqs2 10, Maven 3.6.3, Meson 0.53.1, MethylDackel 0.5.0, Mono 6.8.0.105, medaka 0.12.0, + Nextflow 20.01.0, ncdf4 1.17, netcdf4-python 1.5.3, nodejs 12.16.1, numba 0.47.0, numexpr 2.7.1, + Octave 5.1.0, OpenBLAS 0.3.8, OpenBabel 3.0.0, OpenCV 4.2.0, OpenFOAM-Extend 4.1-20191120, OrthoFinder 2.3.11, + PETSc 3.12.4, PGI 19.10, PMIx 2.2.1, Pango 1.44.7, PyTables 3.6.1, PyTorch 1.4.0, parasail 2.4.1, + pydicom 1.4.2, pyproj 2.4.2, Qhull 2019.1, QuantumESPRESSO 6.5, R-bundle-Bioconductor 3.10, RDKit 2019.09.3 + Racon 1.4.10, ReFrame 2.21, Ruby 2.7.1, rjags 4-9, rpy2 3.2.6, SLEPc 3.12.2, SPAdes 3.14.0, + SPAdes 3.14.0, STAR-Fusion 1.8.1, STAR 2.7.3a, Seaborn 0.10.0, SeqAn 1.4.2, Seurat 3.1.2, SimpleElastix 1.1.0, + SimpleITK 1.2.4, Stacks 2.5, Stata 16, StringTie 2.1.0, scikit-optimize 0.7.4, statsmodels 0.11.0, + TensorFlow 1.15.2 + 2.0.1, Tkinter 2.7.16, Trim_Galore 0.6.5, Trimmomatic 0.39, Trinity 2.10.0, tbb 2020.2, + tqdm 4.41.1, XCrySDen 1.6.2, XGBoost 0.90, xarray 0.15.1, xmlf90 1.5.4 + +* minor enhancements, including: + + * add easyconfig for Java 11.0.6 on ``ppc64le`` and alter the Java 11 wrapper to support both x86_64 and ppc64le (`#9371 `_) + * add additional extensions for R: ``HiddenMarkov`` (`#9685 `_), ``lmerTest`` (`#9853 `_), ``VSURF`` + ``Rborist`` (`#10355 `_) + * change Mesa 19.1.7 + 19.2.1 easyconfigs to use custom easyblock for Mesa (`#9764 `_) + * build shared libs and install header files for Ghostscript (`#9785 `_) + * add MUMPS as dependency in PETSc 3.12.4 easyconfigs (#9880, `#9891 `_) + * add Perl extensions: ``Term::ReadLine::Gnu`` (`#9901 `_), ``URI::Escape`` and ``Set::IntervalTree`` (`#10049 `_) + * add dat directory to aNCI (`#9929 `_) + * add patch to create a symlink from ``libsvm.so.$(SHVER)`` to ``libsvm.so`` in LIBSVM easyconfigs (`#10045 `_) + * build SUNDIALS with '``pic``' (`#10278 `_) + * add ``BSgenome.Hsapiens.UCSC.hg38`` + ``MEDIPS`` extensions to R-bundle-Bioconductor v3.10 (`#10298 `_) + * fix checksums for ``mkl-dnn`` and ``tbb`` extensions (moved to oneAPI repo) in PyTorch easyconfigs (`#10367 `_) + * update ``Java/1.8`` wrapper to ``Java/1.8.0_241.eb`` (`#10305 `_) + +* various bug fixes, including: + + * use CMake for building double-conversion (`#9659 `_) + * update recent libdrm easyconfigs to use custom easyblock & avoid hardcoded x86-specific sanity check (`#9694 `_) + * add alternate checksum for OpenMolcas 18.09 (`#9701 `_) + * use Github to download releases for MariaDB-connector-c (`#9702 `_) + * add ``-DOMPI_SKIP_MPICXX`` in ``configopts`` for MathGL, to avoid using mpicxx during build (`#9703 `_) + * make installing independent of build folder in pybind11 easyconfig (`#9738 `_) + * add Lua as a dependency to gnuplot (`#9773 `_) + * stick to ``http://`` source URLS for ISL in GCCcore easyconfigs, since ``https://`` doesn't work (`#9784 `_) + * add alternative checksums for ``farver``/``fracdiff``/``pkgmaker``/``rngtools``/``doRNG``/``cobs`` extensions in R 3.6.2 easyconfigs (`#9789 `_) + * add patch for OpenBLAS 0.3.4 w/ GCC/8.2.0-2.31.1 to fix broken tests (`#9865 `_) + * revert removal of AVX512 vmovd with 64-bit operands in binutils 2.32 easyconfigs (`#9866 `_) + * fix inline asm in dscal: mark x, x1 as clobbered, in OpenBLAS 0.3.8 (`#9867 `_) + * add missing ``sanity_check_commands`` to cutadapt v1.18 and v2.7 easyconfigs (`#9869 `_) + * don't overwrite ``configopts`` in BLAST+ easyconfigs, append to it (`#9875 `_) + * add alternate checksum for ``LaplacesDemon`` in R 3.6.x easyconfigs (#9879, `#10382 `_) + * fix redefining of preconfigopts in OpenCV easyconfigs (`#9895 `_) + * use symlinks for terminfo files instead of hard links in ncurses 6.1 easyconfigs (`#9912 `_) + * fix NCIPLOT build flags (`#9915 `_) + * add missing patch to iccifort libxc easyconfigs (`#9918 `_) + * use ``checkout@v2`` in GitHub Actions to fix broken re-triggered tests (`#9925 `_) + * re-enable building utils in Siesta 4.1-MaX-1.0 release (`#9936 `_) + * fix homepage and source URLs in SLEPc easyconfigs by using https (`#9943 `_) + * fix source URLs for rgeos after source tarball was moved to CRAN archive (`#9954 `_) + * add dependencies on Python 3 and SciPy-bundle in Trinity v2.9.1 easyconfig (`#9957 `_) + * patch GCC ``lisanitizer`` for glibc 2.31 (`#9966 `_) + * add Zip as build dependency for recent Bazel versions (`#9972 `_) + * fix checksums in Jellyfish v2.3.0 easyconfigs (`#9997 `_) + * fix source URLs for ParMGridGen easyconfigs (`#10019 `_) + * disable unintended Octave support in all libsndfile easyconfigs (`#10027 `_) + * fix sources for LS-PrePost 4.6 (`#10236 `_) + * security update for vsc-mympirun 4.1.9 (`#10185 `_) + * configure libwebp to also install ``libwebpmux`` (`#10274 `_) + * ensure that CVS easyconfigs are included in source tarball produced by '``python setup.py sdist``' (`#10326 `_) + * fix undefined reference error due to libxc 4.3.4 built with CMake (`#10356 `_) + * fix source_urls for tbb: use (new) official '``oneapi-src``' GitHub repository (`#10361 `_) + * add missing build dependency on pkg-config in GObject-Introspection 1.63.1 w/ Python 3.7.4 easyconfig (`#10380 `_) + * update checksums and homepage in tbb easyconfigs (`#10285 `_) + +* other changes: + + * use new custom easyblock in recent CMake easyconfigs (#9871, `#9923 `_) + * add check for redefined easyconfig parameters in easyconfig tests (`#9876 `_) + * use M4-1.4.18.eb for test installation in easyconfigs test suite (`#9926 `_) + * use ``https://`` in ``homepage``/``source_urls`` of ``zlib-1.2.11.eb`` (`#10018 `_) + * add ``-GCCcore-9.2.0`` versionsuffix for ``intel/2020.00`` components (`#10083 `_) + * add checksum of new tbb 2019_U9 source tarball, next to original one + update homepage (`#10237 `_) + * add comment informing about manually setting Gallium drivers in easyconfigs for Mesa v19.1.7 and v19.2.1 (`#10276 `_) + + .. _release_notes_eb412: EasyBuild v4.1.2 (March 16th 2020) diff --git a/docs/Writing_easyconfig_files.rst b/docs/Writing_easyconfig_files.rst index f2c4dbd7..edd0aff4 100644 --- a/docs/Writing_easyconfig_files.rst +++ b/docs/Writing_easyconfig_files.rst @@ -408,28 +408,28 @@ If a recursive checkout should be made of the repository, the ``recursive`` key Examples: * creating a source tarball named ``example-master.tar.gz`` of the ``master`` branch of a (fictional) - ``test`` repository from ``https://github.com/example``: + ``test`` repository from ``https://agitserver.org/example``: .. code:: sources = [{ 'filename': 'example-master.tar.gz', 'git_config': { - 'url': 'https://github.com/example', + 'url': 'https://agitserver.org/example', 'repo_name': 'test', 'tag': 'master', }, }] * creating a source tarball named ``example-20180920.tar.gz`` of the recursive checkout of commit ``abcdef12`` - of the ``test`` repository from ``https://github.com/example``: + of the ``test`` repository from ``https://agitserver.org/example``: .. code:: sources = [{ 'filename': 'example-20180920.tar.gz', 'git_config': { - 'url': 'https://github.com/example', + 'url': 'https://agitserver.org/example', 'repo_name': 'test', 'commit': 'abcdef12', 'recursive': True, @@ -440,8 +440,9 @@ Examples: .. note:: Because the source tarball is created locally (by running ``tar cfvz`` on the directory containing the cloned repository), the (SHA256) checksum is not guaranteed to be the same across different systems. - Whenever you have the option to download a source tarball (or equivalent) directly (for example from GitHub), - we strongly recommend you to do so. + Whenever you have the option to download a source tarball (or equivalent) directly (for example from GitHub, + which also allows downloading a tarball of a specific commit), we strongly recommend you to do so, + ``git_config`` is intended for other Git repos. .. _dependency_specs: diff --git a/docs/conf.py b/docs/conf.py index 1ed64c26..b2f8f013 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -41,9 +41,9 @@ # other places throughout the built documents. # # The short X.Y version. -version = '4.1.2' # this is meant to reference the version of EasyBuild +version = '4.2.0' # this is meant to reference the version of EasyBuild # The full version, including alpha/beta/rc tags. -release = '20200316.0' # this is meant to reference the version of the documentation itself +release = '20200414.0' # this is meant to reference the version of the documentation itself # There are two options for replacing |today|: either, you set today to some # non-false value, then it is used: diff --git a/docs/index.rst b/docs/index.rst index 8ef66668..50f51df0 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -4,7 +4,6 @@ .. EasyBuild documentation master file EasyBuild documentation -======================= Welcome to the documentation of `EasyBuild `_, a software build and installation framework that allows you to manage (scientific) software on High Performance Computing (HPC) systems in an efficient way. @@ -65,12 +64,14 @@ Advanced usage topics Cray-support Detecting_loaded_modules Easyconfig-files-local-variables + Easyconfigs_index Experimental_features Extended_dry_run Hooks Implementing-easyblocks Including_additional_Python_modules Integration_with_GitHub + Locks Manipulating_dependencies Packaging_support Partial_installations diff --git a/docs/version-specific/Supported_software.rst b/docs/version-specific/Supported_software.rst index af1167be..0e08fd78 100644 --- a/docs/version-specific/Supported_software.rst +++ b/docs/version-specific/Supported_software.rst @@ -3,7 +3,7 @@ List of supported software ========================== -EasyBuild |version| supports 1798 different software packages (incl. toolchains, bundles): +EasyBuild |version| supports 1912 different software packages (incl. toolchains, bundles): :ref:`list_software_letter_a` - :ref:`list_software_letter_b` - :ref:`list_software_letter_c` - :ref:`list_software_letter_d` - :ref:`list_software_letter_e` - :ref:`list_software_letter_f` - :ref:`list_software_letter_g` - :ref:`list_software_letter_h` - :ref:`list_software_letter_i` - :ref:`list_software_letter_j` - :ref:`list_software_letter_k` - :ref:`list_software_letter_l` - :ref:`list_software_letter_m` - :ref:`list_software_letter_n` - :ref:`list_software_letter_o` - :ref:`list_software_letter_p` - :ref:`list_software_letter_q` - :ref:`list_software_letter_r` - :ref:`list_software_letter_s` - :ref:`list_software_letter_t` - :ref:`list_software_letter_u` - :ref:`list_software_letter_v` - :ref:`list_software_letter_w` - :ref:`list_software_letter_x` - :ref:`list_software_letter_y` - :ref:`list_software_letter_z` @@ -65,7 +65,7 @@ version toolchain --- -:ref:`list_software_ABAQUS_445` - :ref:`list_software_ABINIT_439` - :ref:`list_software_ABySS_418` - :ref:`list_software_ack_303` - :ref:`list_software_ACT_216` - :ref:`list_software_ACTC_283` - :ref:`list_software_ada_294` - :ref:`list_software_AdapterRemoval_1431` - :ref:`list_software_ADDA_266` - :ref:`list_software_ADF_203` - :ref:`list_software_adjustText_1072` - :ref:`list_software_ADMIXTURE_691` - :ref:`list_software_ADOL-C_400` - :ref:`list_software_Advisor_728` - :ref:`list_software_AFNI_286` - :ref:`list_software_AGFusion_764` - :ref:`list_software_aiohttp_761` - :ref:`list_software_ALADIN_425` - :ref:`list_software_Albacore_793` - :ref:`list_software_ALFA_276` - :ref:`list_software_alleleCount_1144` - :ref:`list_software_Allinea_694` - :ref:`list_software_ALLPATHS-LG_793` - :ref:`list_software_ALPS_304` - :ref:`list_software_Amara_482` - :ref:`list_software_amask_525` - :ref:`list_software_Amber_487` - :ref:`list_software_AmberMini_884` - :ref:`list_software_AmberTools_1016` - :ref:`list_software_AMD-LibM_611` - :ref:`list_software_AMD-RNG_486` - :ref:`list_software_AMD-SecureRNG_1101` - :ref:`list_software_AMOS_304` - :ref:`list_software_AMPL-MP_500` - :ref:`list_software_Anaconda2_839` - :ref:`list_software_Anaconda3_840` - :ref:`list_software_angsd_525` - :ref:`list_software_Annif_492` - :ref:`list_software_annovar_757` - :ref:`list_software_ANSYS_398` - :ref:`list_software_ANSYS_CFD_698` - :ref:`list_software_ant_323` - :ref:`list_software_ANTLR_385` - :ref:`list_software_ANTs_342` - :ref:`list_software_anvio_541` - :ref:`list_software_APBS_294` - :ref:`list_software_APR_227` - :ref:`list_software_APR-util_718` - :ref:`list_software_ARAGORN_522` - :ref:`list_software_Arb_277` - :ref:`list_software_ARCH_286` - :ref:`list_software_ARGoS_412` - :ref:`list_software_argtable_834` - :ref:`list_software_Armadillo_917` - :ref:`list_software_ARPACK++_520` - :ref:`list_software_arpack-ng_884` - :ref:`list_software_ArrayFire_901` - :ref:`list_software_Arriba_593` - :ref:`list_software_Arrow_523` - :ref:`list_software_ART_231` - :ref:`list_software_ARWEN_381` - :ref:`list_software_ASAP3_344` - :ref:`list_software_ASE_217` - :ref:`list_software_ASHS_303` - :ref:`list_software_Aspera-CLI_865` - :ref:`list_software_Aspera-Connect_1363` - :ref:`list_software_Assimulo_845` - :ref:`list_software_ASTRID_455` - :ref:`list_software_astropy_786` - :ref:`list_software_at-spi2-atk_1005` - :ref:`list_software_at-spi2-core_1110` - :ref:`list_software_ATK_224` - :ref:`list_software_ATLAS_373` - :ref:`list_software_atomate_747` - :ref:`list_software_AtomPAW_633` - :ref:`list_software_atools_658` - :ref:`list_software_ATSAS_380` - :ref:`list_software_attr_443` - :ref:`list_software_AUGUSTUS_641` - :ref:`list_software_Autoconf_831` - :ref:`list_software_Autoconf-archive_1614` - :ref:`list_software_AutoDock_794` - :ref:`list_software_AutoDock_Vina_1287` - :ref:`list_software_AutoGrid_799` - :ref:`list_software_Automake_823` - :ref:`list_software_Autotools_970` - :ref:`list_software_awscli_643` +:ref:`list_software_ABAQUS_445` - :ref:`list_software_ABINIT_439` - :ref:`list_software_ABRA2_328` - :ref:`list_software_ABRicate_731` - :ref:`list_software_ABySS_418` - :ref:`list_software_ack_303` - :ref:`list_software_ACT_216` - :ref:`list_software_ACTC_283` - :ref:`list_software_ada_294` - :ref:`list_software_AdapterRemoval_1431` - :ref:`list_software_ADDA_266` - :ref:`list_software_ADF_203` - :ref:`list_software_ADIOS_368` - :ref:`list_software_adjustText_1072` - :ref:`list_software_ADMIXTURE_691` - :ref:`list_software_ADOL-C_400` - :ref:`list_software_Advisor_728` - :ref:`list_software_AFNI_286` - :ref:`list_software_AGFusion_764` - :ref:`list_software_aiohttp_761` - :ref:`list_software_ALADIN_425` - :ref:`list_software_Albacore_793` - :ref:`list_software_ALFA_276` - :ref:`list_software_alleleCount_1144` - :ref:`list_software_Allinea_694` - :ref:`list_software_ALLPATHS-LG_793` - :ref:`list_software_ALPS_304` - :ref:`list_software_Amara_482` - :ref:`list_software_amask_525` - :ref:`list_software_Amber_487` - :ref:`list_software_AmberMini_884` - :ref:`list_software_AmberTools_1016` - :ref:`list_software_AMD-LibM_611` - :ref:`list_software_AMD-RNG_486` - :ref:`list_software_AMD-SecureRNG_1101` - :ref:`list_software_AMOS_304` - :ref:`list_software_AMPL-MP_500` - :ref:`list_software_Anaconda2_839` - :ref:`list_software_Anaconda3_840` - :ref:`list_software_aNCI_315` - :ref:`list_software_angsd_525` - :ref:`list_software_Annif_492` - :ref:`list_software_annovar_757` - :ref:`list_software_ANSYS_398` - :ref:`list_software_ANSYS_CFD_698` - :ref:`list_software_ant_323` - :ref:`list_software_ANTLR_385` - :ref:`list_software_ANTs_342` - :ref:`list_software_anvio_541` - :ref:`list_software_any2fasta_905` - :ref:`list_software_APBS_294` - :ref:`list_software_apex_430` - :ref:`list_software_APR_227` - :ref:`list_software_APR-util_718` - :ref:`list_software_ARAGORN_522` - :ref:`list_software_Arb_277` - :ref:`list_software_ARCH_286` - :ref:`list_software_archspec_841` - :ref:`list_software_ARGoS_412` - :ref:`list_software_argtable_834` - :ref:`list_software_Armadillo_917` - :ref:`list_software_ARPACK++_520` - :ref:`list_software_arpack-ng_884` - :ref:`list_software_ArrayFire_901` - :ref:`list_software_Arriba_593` - :ref:`list_software_Arrow_523` - :ref:`list_software_ART_231` - :ref:`list_software_ArviZ_492` - :ref:`list_software_ARWEN_381` - :ref:`list_software_ASAP3_344` - :ref:`list_software_ASE_217` - :ref:`list_software_ASHS_303` - :ref:`list_software_Aspera-CLI_865` - :ref:`list_software_Aspera-Connect_1363` - :ref:`list_software_Assimulo_845` - :ref:`list_software_ASTRID_455` - :ref:`list_software_astropy_786` - :ref:`list_software_at-spi2-atk_1005` - :ref:`list_software_at-spi2-core_1110` - :ref:`list_software_ATK_224` - :ref:`list_software_ATLAS_373` - :ref:`list_software_atomate_747` - :ref:`list_software_AtomPAW_633` - :ref:`list_software_atools_658` - :ref:`list_software_ATSAS_380` - :ref:`list_software_attr_443` - :ref:`list_software_AUGUSTUS_641` - :ref:`list_software_Autoconf_831` - :ref:`list_software_Autoconf-archive_1614` - :ref:`list_software_AutoDock_794` - :ref:`list_software_AutoDock_Vina_1287` - :ref:`list_software_AutoGrid_799` - :ref:`list_software_Automake_823` - :ref:`list_software_autopep8_822` - :ref:`list_software_Autotools_970` - :ref:`list_software_awscli_643` .. _list_software_ABAQUS_445: @@ -115,6 +115,39 @@ version versionsuffix toolchain ========== ======================== =============================== +.. _list_software_ABRA2_328: + +*ABRA2* ++++++++ + +Assembly Based ReAligner + +*homepage*: https://github.com/mozack/abra2 + +======== ======================= +version toolchain +======== ======================= +``2.22`` ``iccifort/2019.5.281`` +======== ======================= + + +.. _list_software_ABRicate_731: + +*ABRicate* +++++++++++ + +Mass screening of contigs for antimicrobial and virulence genes + +*homepage*: https://github.com/tseemann/abricate + +========= ================ =============== +version versionsuffix toolchain +========= ================ =============== +``0.9.9`` ``gompi/2019b`` +``0.9.9`` ``-Perl-5.28.1`` ``gompi/2019a`` +========= ================ =============== + + .. _list_software_ABySS_418: *ABySS* @@ -122,7 +155,7 @@ version versionsuffix toolchain Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler -*homepage*: http://www.bcgsc.ca/platform/bioinfo/software/abyss +*homepage*: https://www.bcgsc.ca/platform/bioinfo/software/abyss ========= ================================================================ version toolchain @@ -130,6 +163,7 @@ version toolchain ``1.9.0`` ``foss/2016a`` ``2.0.2`` ``foss/2016b``, ``foss/2018a``, ``gompi/2019a``, ``intel/2016b`` ``2.0.3`` ``foss/2017b``, ``intel/2017b`` +``2.1.5`` ``foss/2019b`` ========= ================================================================ @@ -251,6 +285,22 @@ version toolchain ================================ =============== +.. _list_software_ADIOS_368: + +*ADIOS* ++++++++ + +The Adaptable IO System (ADIOS) provides a simple, flexible way for scientists to describe the data in their code that may need to be written, read, or processed outside of the running simulation. + +*homepage*: https://www.olcf.ornl.gov/center-projects/adios/ + +========== ================== ============== +version versionsuffix toolchain +========== ================== ============== +``1.13.1`` ``-Python-2.7.15`` ``foss/2019a`` +========== ================== ============== + + .. _list_software_adjustText_1072: *adjustText* @@ -706,6 +756,22 @@ version toolchain =========== ========== +.. _list_software_aNCI_315: + +*aNCI* +++++++ + +Non-covalent interaction (NCI) for MD trajectories + +*homepage*: https://www.lct.jussieu.fr/pagesperso/contrera/nci-MD.html + +======= ======================= +version toolchain +======= ======================= +``2.0`` ``iccifort/2019.5.281`` +======= ======================= + + .. _list_software_angsd_525: *angsd* @@ -853,7 +919,7 @@ version versionsuffix toolchain ANTs extracts information from complex datasets that include imaging. ANTs is useful for managing, interpreting and visualizing multidimensional data. -*homepage*: http://stnava.github.io/ANTs/ +*homepage*: https://stnava.github.io/ANTs/ ========= ================== =============================== version versionsuffix toolchain @@ -861,6 +927,7 @@ version versionsuffix toolchain ``2.2.0`` ``-Python-2.7.12`` ``foss/2016b`` ``2.3.0`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` ``2.3.1`` ``-Python-3.6.6`` ``foss/2018b`` +``2.3.2`` ``-Python-3.7.4`` ``foss/2019b`` ========= ================== =============================== @@ -880,6 +947,23 @@ version versionsuffix toolchain ======= ================= =============== +.. _list_software_any2fasta_905: + +*any2fasta* ++++++++++++ + +Convert various sequence formats to FASTA + +*homepage*: https://github.com/tseemann/any2fasta + +========= ================ ================= +version versionsuffix toolchain +========= ================ ================= +``0.4.2`` ``GCCcore/8.3.0`` +``0.4.2`` ``-Perl-5.28.1`` ``GCCcore/8.2.0`` +========= ================ ================= + + .. _list_software_APBS_294: *APBS* @@ -896,6 +980,22 @@ version versionsuffix toolchain ======= ======================== ========== +.. _list_software_apex_430: + +*apex* +++++++ + +A PyTorch Extension: Tools for easy mixed precision and distributed training in Pytorch + +*homepage*: https://github.com/nvidia/apex + +============ ================= ================== +version versionsuffix toolchain +============ ================= ================== +``20200325`` ``-Python-3.7.4`` ``fosscuda/2019b`` +============ ================= ================== + + .. _list_software_APR_227: *APR* @@ -977,6 +1077,22 @@ version versionsuffix toolchain ========= ================= =============== +.. _list_software_archspec_841: + +*archspec* +++++++++++ + +A library for detecting, labeling, and reasoning about microarchitectures + +*homepage*: https://github.com/archspec/archspec + +========= ================= ================= +version versionsuffix toolchain +========= ================= ================= +``0.1.0`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` +========= ================= ================= + + .. _list_software_ARGoS_412: *ARGoS* @@ -1002,11 +1118,11 @@ Argtable is an ANSI C library for parsing GNU style command line options with a *homepage*: http://argtable.sourceforge.net/ -======== =================================================================================== -version toolchain -======== =================================================================================== -``2.13`` ``GCCcore/8.2.0``, ``foss/2016b``, ``foss/2018b``, ``intel/2018a``, ``intel/2018b`` -======== =================================================================================== +======== ====================================================================================================== +version toolchain +======== ====================================================================================================== +``2.13`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``foss/2016b``, ``foss/2018b``, ``intel/2018a``, ``intel/2018b`` +======== ====================================================================================================== .. _list_software_Armadillo_917: @@ -1062,7 +1178,7 @@ version toolchain ``3.4.0`` ``foss/2016b``, ``foss/2017a``, ``intel/2016b``, ``intel/2017a`` ``3.5.0`` ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``intel/2017a``, ``intel/2017b`` ``3.6.2`` ``intel/2018a`` -``3.7.0`` ``foss/2019a``, ``foss/2019b`` +``3.7.0`` ``foss/2019a``, ``foss/2019b``, ``intel/2019b`` ========= ================================================================================ @@ -1114,6 +1230,7 @@ version versionsuffix toolchain ``0.7.1`` ``-Python-3.6.3`` ``intel/2017b`` ``0.12.0`` ``-Python-2.7.15`` ``foss/2018b``, ``intel/2018b`` ``0.12.0`` ``-Python-3.6.6`` ``intel/2018b`` +``0.16.0`` ``-Python-3.7.4`` ``intel/2019b`` ========== ================== =============================== @@ -1133,6 +1250,22 @@ version toolchain ============== ================================== +.. _list_software_ArviZ_492: + +*ArviZ* ++++++++ + +Exploratory analysis of Bayesian models with Python + +*homepage*: https://github.com/arviz-devs/arviz + +========= ================= =============== +version versionsuffix toolchain +========= ================= =============== +``0.7.0`` ``-Python-3.7.4`` ``intel/2019b`` +========= ================= =============== + + .. _list_software_ARWEN_381: *ARWEN* @@ -1199,6 +1332,8 @@ version versionsuffix toolchain ``3.17.0`` ``-Python-3.7.2`` ``foss/2019a``, ``intel/2019a`` ``3.18.0`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` ``3.18.0`` ``-Python-3.7.2`` ``foss/2019a``, ``intel/2019a`` +``3.19.0`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` +``3.19.0`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` ============== ================== ================================================ @@ -1315,6 +1450,7 @@ version toolchain ========== ================== ``2.26.3`` ``fosscuda/2018b`` ``2.32.0`` ``GCCcore/8.2.0`` +``2.34.1`` ``GCCcore/8.3.0`` ========== ================== @@ -1332,6 +1468,7 @@ version toolchain ========== ================== ``2.26.3`` ``fosscuda/2018b`` ``2.32.0`` ``GCCcore/8.2.0`` +``2.34.0`` ``GCCcore/8.3.0`` ========== ================== @@ -1342,7 +1479,7 @@ version toolchain ATK provides the set of accessibility interfaces that are implemented by other toolkits and applications. Using the ATK interfaces, accessibility tools have full access to view and control running applications. -*homepage*: https://developer.gnome.org/ATK/stable/ +*homepage*: https://developer.gnome.org/atk/ ========== =================================================================== version toolchain @@ -1355,6 +1492,7 @@ version toolchain ``2.27.1`` ``foss/2017b``, ``intel/2017b`` ``2.28.1`` ``foss/2018a``, ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018a`` ``2.32.0`` ``GCCcore/8.2.0`` +``2.34.1`` ``GCCcore/8.3.0`` ========== =================================================================== @@ -1476,6 +1614,7 @@ version versionsuffix toolchain ``3.3.2`` ``-Python-2.7.13`` ``intel/2017a`` ``3.3.2`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` ``3.3.2`` ``-Python-2.7.15`` ``intel/2018b`` +``3.3.3`` ``foss/2019b`` ========= ================== =============================== @@ -1581,6 +1720,22 @@ version toolchain ========== ===================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== +.. _list_software_autopep8_822: + +*autopep8* +++++++++++ + +A tool that automatically formats Python code to conform to the PEP 8 style guide. + +*homepage*: https://github.com/hhatto/autopep8 + +========= ================= =============== +version versionsuffix toolchain +========= ================= =============== +``1.4.4`` ``-Python-3.6.4`` ``intel/2018a`` +========= ================= =============== + + .. _list_software_Autotools_970: *Autotools* @@ -1609,13 +1764,14 @@ Universal Command Line Environment for AWS *homepage*: https://pypi.python.org/pypi/awscli -============ ================== =============== -version versionsuffix toolchain -============ ================== =============== -``1.11.1`` ``-Python-2.7.12`` ``intel/2016b`` -``1.11.56`` ``-Python-2.7.12`` ``foss/2016b`` -``1.16.290`` ``-Python-3.6.6`` ``foss/2018b`` -============ ================== =============== +============ ================== ================= +version versionsuffix toolchain +============ ================== ================= +``1.11.1`` ``-Python-2.7.12`` ``intel/2016b`` +``1.11.56`` ``-Python-2.7.12`` ``foss/2016b`` +``1.16.290`` ``-Python-3.6.6`` ``foss/2018b`` +``1.17.7`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` +============ ================== ================= .. _list_software_letter_b: @@ -1624,7 +1780,7 @@ version versionsuffix toolchain --- -:ref:`list_software_Bader_478` - :ref:`list_software_BAGEL_347` - :ref:`list_software_bam-readcount_1314` - :ref:`list_software_BAMM_285` - :ref:`list_software_BamM_349` - :ref:`list_software_BamTools_801` - :ref:`list_software_BamUtil_686` - :ref:`list_software_Bandage_674` - :ref:`list_software_barrnap_742` - :ref:`list_software_basemap_729` - :ref:`list_software_Bash_382` - :ref:`list_software_bat_311` - :ref:`list_software_BayesAss_795` - :ref:`list_software_BayeScan_774` - :ref:`list_software_BayeScEnv_864` - :ref:`list_software_BayesTraits_1131` - :ref:`list_software_Bazel_494` - :ref:`list_software_bbcp_407` - :ref:`list_software_bbFTP_430` - :ref:`list_software_BBMap_418` - :ref:`list_software_bc_197` - :ref:`list_software_BCALM_351` - :ref:`list_software_BCEL_278` - :ref:`list_software_BCFtools_764` - :ref:`list_software_bcgTree_700` - :ref:`list_software_bcl2fastq2_948` - :ref:`list_software_bcolz_538` - :ref:`list_software_BDBag_400` - :ref:`list_software_beagle-lib_964` - :ref:`list_software_Beast_495` - :ref:`list_software_BeautifulSoup_1352` - :ref:`list_software_BEDOPS_445` - :ref:`list_software_BEDTools_732` - :ref:`list_software_behave_619` - :ref:`list_software_BerkeleyGW_977` - :ref:`list_software_BFAST_368` - :ref:`list_software_BFC_203` - :ref:`list_software_bibtexparser_1291` - :ref:`list_software_binutils_874` - :ref:`list_software_Bio-DB-HTS_745` - :ref:`list_software_Bio-SamTools_1145` - :ref:`list_software_bioawk_637` - :ref:`list_software_biobambam2_972` - :ref:`list_software_biomart-perl_1230` - :ref:`list_software_BioPerl_685` - :ref:`list_software_Biopython_956` - :ref:`list_software_biscuit_755` - :ref:`list_software_Bismark_713` - :ref:`list_software_Bison_507` - :ref:`list_software_bitarray_862` - :ref:`list_software_BLACS_357` - :ref:`list_software_BLASR_372` - :ref:`list_software_blasr_libcpp_1261` - :ref:`list_software_BLAST_374` - :ref:`list_software_BLAST+_417` - :ref:`list_software_BLAT_291` - :ref:`list_software_Blender_700` - :ref:`list_software_BLIS_298` - :ref:`list_software_Blitz++_603` - :ref:`list_software_BlobTools_912` - :ref:`list_software_Blosc_499` - :ref:`list_software_bmtagger_841` - :ref:`list_software_bnpy_441` - :ref:`list_software_BOINC_363` - :ref:`list_software_bokeh_521` - :ref:`list_software_BoltzTraP_898` - :ref:`list_software_Bonmin_611` - :ref:`list_software_Bonnie++_689` - :ref:`list_software_Boost_519` - :ref:`list_software_Boost.Python_1207` - :ref:`list_software_Bottleneck_1035` - :ref:`list_software_Bowtie_618` - :ref:`list_software_Bowtie2_668` - :ref:`list_software_Bpipe_496` - :ref:`list_software_bpp-core_792` - :ref:`list_software_bpp-phyl_812` - :ref:`list_software_bpp-seq_696` - :ref:`list_software_BRAKER_439` - :ref:`list_software_BreakDancer_1074` - :ref:`list_software_breseq_642` - :ref:`list_software_bsddb3_562` - :ref:`list_software_buildenv_857` - :ref:`list_software_Bullet_616` - :ref:`list_software_BUSCO_380` - :ref:`list_software_BWA_218` - :ref:`list_software_bwa-meth_789` - :ref:`list_software_bwakit_642` - :ref:`list_software_bwidget_742` - :ref:`list_software_BWISE_378` - :ref:`list_software_bx-python_937` - :ref:`list_software_BXH_XCEDE_TOOLS_1178` - :ref:`list_software_byacc_514` - :ref:`list_software_bzip2_487` +:ref:`list_software_Bader_478` - :ref:`list_software_BAGEL_347` - :ref:`list_software_bam-readcount_1314` - :ref:`list_software_BAMM_285` - :ref:`list_software_BamM_349` - :ref:`list_software_BAMSurgeon_947` - :ref:`list_software_BamTools_801` - :ref:`list_software_BamUtil_686` - :ref:`list_software_Bandage_674` - :ref:`list_software_barrnap_742` - :ref:`list_software_basemap_729` - :ref:`list_software_Bash_382` - :ref:`list_software_bat_311` - :ref:`list_software_BatMeth2_727` - :ref:`list_software_BayesAss_795` - :ref:`list_software_BayeScan_774` - :ref:`list_software_BayeScEnv_864` - :ref:`list_software_BayesTraits_1131` - :ref:`list_software_Bazel_494` - :ref:`list_software_bbcp_407` - :ref:`list_software_bbFTP_430` - :ref:`list_software_BBMap_418` - :ref:`list_software_bc_197` - :ref:`list_software_BCALM_351` - :ref:`list_software_BCEL_278` - :ref:`list_software_BCFtools_764` - :ref:`list_software_bcgTree_700` - :ref:`list_software_bcl2fastq2_948` - :ref:`list_software_bcolz_538` - :ref:`list_software_BDBag_400` - :ref:`list_software_beagle-lib_964` - :ref:`list_software_Beast_495` - :ref:`list_software_BeautifulSoup_1352` - :ref:`list_software_BEDOPS_445` - :ref:`list_software_BEDTools_732` - :ref:`list_software_behave_619` - :ref:`list_software_BerkeleyGW_977` - :ref:`list_software_BFAST_368` - :ref:`list_software_BFC_203` - :ref:`list_software_bibtexparser_1291` - :ref:`list_software_BiG-SCAPE_651` - :ref:`list_software_BinSanity_913` - :ref:`list_software_binutils_874` - :ref:`list_software_Bio-DB-HTS_745` - :ref:`list_software_Bio-SamTools_1145` - :ref:`list_software_bioawk_637` - :ref:`list_software_biobambam2_972` - :ref:`list_software_biomart-perl_1230` - :ref:`list_software_BioPerl_685` - :ref:`list_software_Biopython_956` - :ref:`list_software_biscuit_755` - :ref:`list_software_Bismark_713` - :ref:`list_software_Bison_507` - :ref:`list_software_bitarray_862` - :ref:`list_software_BLACS_357` - :ref:`list_software_BLASR_372` - :ref:`list_software_blasr_libcpp_1261` - :ref:`list_software_BLAST_374` - :ref:`list_software_BLAST+_417` - :ref:`list_software_BLAT_291` - :ref:`list_software_Blender_700` - :ref:`list_software_BLIS_298` - :ref:`list_software_Blitz++_603` - :ref:`list_software_BlobTools_912` - :ref:`list_software_Blosc_499` - :ref:`list_software_bmtagger_841` - :ref:`list_software_bnpy_441` - :ref:`list_software_BOINC_363` - :ref:`list_software_bokeh_521` - :ref:`list_software_BoltzTraP_898` - :ref:`list_software_Bonito_619` - :ref:`list_software_Bonmin_611` - :ref:`list_software_Bonnie++_689` - :ref:`list_software_Boost_519` - :ref:`list_software_Boost.Python_1207` - :ref:`list_software_Bottleneck_1035` - :ref:`list_software_Bowtie_618` - :ref:`list_software_Bowtie2_668` - :ref:`list_software_Bpipe_496` - :ref:`list_software_bpp-core_792` - :ref:`list_software_bpp-phyl_812` - :ref:`list_software_bpp-seq_696` - :ref:`list_software_BRAKER_439` - :ref:`list_software_BreakDancer_1074` - :ref:`list_software_breseq_642` - :ref:`list_software_bsddb3_562` - :ref:`list_software_BSMAPz_493` - :ref:`list_software_BSseeker2_838` - :ref:`list_software_buildenv_857` - :ref:`list_software_Bullet_616` - :ref:`list_software_BUSCO_380` - :ref:`list_software_BUStools_795` - :ref:`list_software_BWA_218` - :ref:`list_software_bwa-meth_789` - :ref:`list_software_bwakit_642` - :ref:`list_software_bwidget_742` - :ref:`list_software_BWISE_378` - :ref:`list_software_bx-python_937` - :ref:`list_software_BXH_XCEDE_TOOLS_1178` - :ref:`list_software_byacc_514` - :ref:`list_software_bzip2_487` .. _list_software_Bader_478: @@ -1709,6 +1865,22 @@ version versionsuffix toolchain ========= ================== ============== +.. _list_software_BAMSurgeon_947: + +*BAMSurgeon* +++++++++++++ + +Tools for adding mutations to existing .bam files, used for testing mutation callers + +*homepage*: https://github.com/adamewing/bamsurgeon + +======= ================== ============= +version versionsuffix toolchain +======= ================== ============= +``1.2`` ``-Python-2.7.16`` ``GCC/8.3.0`` +======= ================== ============= + + .. _list_software_BamTools_801: *BamTools* @@ -1718,14 +1890,14 @@ BamTools provides both a programmer's API and an end-user's toolkit for handling *homepage*: https://github.com/pezmaster31/bamtools -========= ================================================================================================================================================ -version toolchain -========= ================================================================================================================================================ -``2.4.0`` ``foss/2016b`` -``2.4.1`` ``intel/2017a`` -``2.5.0`` ``foss/2016b``, ``intel/2017b`` -``2.5.1`` ``GCC/8.2.0-2.31.1``, ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``intel/2017b``, ``intel/2018b`` -========= ================================================================================================================================================ +========= ======================================================================================================================================================================================== +version toolchain +========= ======================================================================================================================================================================================== +``2.4.0`` ``foss/2016b`` +``2.4.1`` ``intel/2017a`` +``2.5.0`` ``foss/2016b``, ``intel/2017b`` +``2.5.1`` ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0``, ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``iccifort/2019.5.281``, ``intel/2017b``, ``intel/2018b`` +========= ======================================================================================================================================================================================== .. _list_software_BamUtil_686: @@ -1829,6 +2001,22 @@ version versionsuffix toolchain ========= ================= =============== +.. _list_software_BatMeth2_727: + +*BatMeth2* +++++++++++ + +An Integrated Package for Bisulfite DNA Methylation Data Analysis with Indel-sensitive Mapping. + +*homepage*: https://github.com/GuoliangLi-HZAU/BatMeth2 + +======= ============== +version toolchain +======= ============== +``2.1`` ``foss/2019b`` +======= ============== + + .. _list_software_BayesAss_795: *BayesAss* @@ -1870,11 +2058,11 @@ BayeScEnv is a Fst-based, genome-scan method that uses environmental variables t *homepage*: https://github.com/devillemereuil/bayescenv -======= ============== -version toolchain -======= ============== -``1.1`` ``foss/2016a`` -======= ============== +======= ====================================================== +version toolchain +======= ====================================================== +``1.1`` ``GCC/8.3.0``, ``foss/2016a``, ``iccifort/2019.5.281`` +======= ====================================================== .. _list_software_BayesTraits_1131: @@ -1970,6 +2158,7 @@ version versionsuffix toolchain ``37.93`` ``foss/2018a``, ``intel/2018a`` ``38.26`` ``foss/2018b`` ``38.50b`` ``GCC/8.2.0-2.31.1`` +``38.76`` ``GCC/8.2.0-2.31.1`` ========== =================== =============================== @@ -2030,13 +2219,14 @@ Samtools is a suite of programs for interacting with high-throughput sequencing *homepage*: http://www.htslib.org/ -======= ========================================================================================= -version toolchain -======= ========================================================================================= -``1.3`` ``foss/2016a``, ``intel/2016a`` -``1.6`` ``foss/2016b``, ``foss/2017b``, ``intel/2017b`` -``1.9`` ``foss/2018a``, ``foss/2018b``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``intel/2018b`` -======= ========================================================================================= +========== ========================================================================================= +version toolchain +========== ========================================================================================= +``1.3`` ``foss/2016a``, ``intel/2016a`` +``1.6`` ``foss/2016b``, ``foss/2017b``, ``intel/2017b`` +``1.9`` ``foss/2018a``, ``foss/2018b``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``intel/2018b`` +``1.10.2`` ``GCC/8.3.0`` +========== ========================================================================================= .. _list_software_bcgTree_700: @@ -2195,9 +2385,9 @@ version toolchain *BEDTools* ++++++++++ -The BEDTools utilities allow one to address common genomics tasks such as finding feature overlaps and computing coverage. The utilities are largely based on four widely-used file formats: BED, GFF/GTF, VCF, and SAM/BAM. +BEDTools: a powerful toolset for genome arithmetic. The BEDTools utilities allow one to address common genomics tasks such as finding feature overlaps and computing coverage. The utilities are largely based on four widely-used file formats: BED, GFF/GTF, VCF, and SAM/BAM. -*homepage*: https://github.com/arq5x/bedtools2 +*homepage*: https://bedtools.readthedocs.io/ ========== ==================================================================================== version toolchain @@ -2206,6 +2396,7 @@ version toolchain ``2.26.0`` ``GCCcore/6.4.0``, ``foss/2016a``, ``intel/2016b``, ``intel/2017a``, ``intel/2017b`` ``2.27.1`` ``GCCcore/6.4.0``, ``foss/2016b``, ``foss/2018b``, ``intel/2017a``, ``intel/2018a`` ``2.28.0`` ``GCC/8.2.0-2.31.1``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1`` +``2.29.2`` ``GCC/8.3.0`` ========== ==================================================================================== @@ -2233,16 +2424,17 @@ version versionsuffix toolchain The BerkeleyGW Package is a set of computer codes that calculates the quasiparticle properties and the optical responses of a large variety of materials from bulk periodic crystals to nanostructures such as slabs, wires and molecules. -*homepage*: http://www.berkeleygw.org +*homepage*: https://www.berkeleygw.org -============= ================================================================ -version toolchain -============= ================================================================ -``1.0.6`` ``intel/2016.02-GCC-4.9`` -``1.1-beta2`` ``intel/2016.02-GCC-4.9`` -``1.2.0`` ``intel/2017a``, ``intel/2018a`` -``2.0.0`` ``foss/2017b``, ``foss/2018b``, ``intel/2017b``, ``intel/2018a`` -============= ================================================================ +============= ================= ================================================================ +version versionsuffix toolchain +============= ================= ================================================================ +``1.0.6`` ``intel/2016.02-GCC-4.9`` +``1.1-beta2`` ``intel/2016.02-GCC-4.9`` +``1.2.0`` ``intel/2017a``, ``intel/2018a`` +``2.0.0`` ``foss/2017b``, ``foss/2018b``, ``intel/2017b``, ``intel/2018a`` +``2.1.0`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` +============= ================= ================================================================ .. _list_software_BFAST_368: @@ -2293,6 +2485,38 @@ version toolchain ========= ================= +.. _list_software_BiG-SCAPE_651: + +*BiG-SCAPE* ++++++++++++ + +BiG-SCAPE and CORASON provide a set of tools to explore the diversity of biosynthetic gene clusters (BGCs) across large numbers of genomes, by constructing BGC sequence similarity networks, grouping BGCs into gene cluster families, and exploring gene cluster diversity linked to enzyme phylogenies. + +*homepage*: https://bigscape-corason.secondarymetabolites.org/index.html + +========= ================= =============== +version versionsuffix toolchain +========= ================= =============== +``1.0.1`` ``-Python-3.7.4`` ``intel/2019b`` +========= ================= =============== + + +.. _list_software_BinSanity_913: + +*BinSanity* ++++++++++++ + +BinSanity contains a suite a scripts designed to cluster contigs generated from metagenomic assembly into putative genomes. + +*homepage*: https://github.com/edgraham/BinSanity/wiki + +========= ================= ============== +version versionsuffix toolchain +========= ================= ============== +``0.3.5`` ``-Python-3.7.4`` ``foss/2019b`` +========= ================= ============== + + .. _list_software_binutils_874: *binutils* @@ -2314,6 +2538,7 @@ version toolchain ``2.30`` ``GCCcore/7.3.0``, ``GCCcore/8.1.0``, ``system`` ``2.31.1`` ``GCCcore/7.4.0``, ``GCCcore/8.2.0``, ``system`` ``2.32`` ``GCCcore/8.3.0``, ``GCCcore/9.1.0``, ``GCCcore/9.2.0``, ``system`` +``2.34`` ``GCCcore/9.3.0``, ``system`` ========== ======================================================================================================================================================================================== @@ -2451,6 +2676,7 @@ version versionsuffix toolchain ``1.73`` ``foss/2019a``, ``fosscuda/2019a``, ``intel/2019a`` ``1.73`` ``-Python-3.6.6`` ``foss/2018b`` ``1.74`` ``foss/2019a`` +``1.75`` ``-Python-2.7.16`` ``foss/2019b`` ``1.75`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` ======== ================== =================================================== @@ -2495,7 +2721,7 @@ version toolchain Bison is a general-purpose parser generator that converts an annotated context-free grammar into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables. -*homepage*: http://www.gnu.org/software/bison +*homepage*: https://www.gnu.org/software/bison ========= ========================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== version toolchain @@ -2506,7 +2732,9 @@ version toolchain ``3.0.4`` ``GCC/4.9.2``, ``GCC/4.9.2-binutils-2.25``, ``GCC/4.9.3``, ``GCC/4.9.3-2.25``, ``GCC/4.9.3-binutils-2.25``, ``GCC/5.1.0-binutils-2.25``, ``GCCcore/4.9.2``, ``GCCcore/4.9.3``, ``GCCcore/4.9.4``, ``GCCcore/5.3.0``, ``GCCcore/5.4.0``, ``GCCcore/5.5.0``, ``GCCcore/6.1.0``, ``GCCcore/6.2.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.1.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.1.0``, ``GCCcore/system``, ``GNU/4.9.3-2.25``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``gimkl/2017a``, ``intel/2016.02-GCC-4.9``, ``intel/2016a``, ``intel/2016b``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25``, ``system`` ``3.0.5`` ``GCCcore/5.5.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.1.0``, ``GCCcore/8.2.0``, ``GCCcore/system``, ``system`` ``3.2.2`` ``GCCcore/7.4.0`` -``3.3.2`` ``GCCcore/8.3.0``, ``GCCcore/9.1.0``, ``GCCcore/9.2.0``, ``system`` +``3.3.2`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.1.0``, ``GCCcore/9.2.0``, ``system`` +``3.5.2`` ``system`` +``3.5.3`` ``GCCcore/9.3.0``, ``system`` ========= ========================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== @@ -2591,6 +2819,7 @@ version versionsuffix toolchain ========== ================= ========== ``2.2.26`` ``-Linux_x86_64`` ``system`` ``2.8.1`` ``-Linux_x86_64`` ``system`` +``2.10.0`` ``-Linux_x86_64`` ``system`` ========== ================= ========== @@ -2601,21 +2830,21 @@ version versionsuffix toolchain Basic Local Alignment Search Tool, or BLAST, is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of different proteins or the nucleotides of DNA sequences. -*homepage*: http://blast.ncbi.nlm.nih.gov/ +*homepage*: https://blast.ncbi.nlm.nih.gov/ -========== ================== ================================================================ -version versionsuffix toolchain -========== ================== ================================================================ -``2.2.31`` ``system`` -``2.3.0`` ``-Python-2.7.11`` ``foss/2016a`` -``2.6.0`` ``-Python-2.7.12`` ``foss/2016b`` -``2.6.0`` ``-Python-2.7.13`` ``foss/2017a``, ``intel/2017a`` -``2.6.0`` ``-Python-2.7.14`` ``intel/2017b`` -``2.7.1`` ``foss/2018a``, ``foss/2018b``, ``intel/2018a``, ``intel/2018b`` -``2.7.1`` ``-Python-2.7.14`` ``intel/2017b`` -``2.8.1`` ``foss/2018b`` -``2.9.0`` ``gompi/2019a``, ``gompi/2019b``, ``iimpi/2019a`` -========== ================== ================================================================ +========== ================== ================================================================== +version versionsuffix toolchain +========== ================== ================================================================== +``2.2.31`` ``system`` +``2.3.0`` ``-Python-2.7.11`` ``foss/2016a`` +``2.6.0`` ``-Python-2.7.12`` ``foss/2016b`` +``2.6.0`` ``-Python-2.7.13`` ``foss/2017a``, ``intel/2017a`` +``2.6.0`` ``-Python-2.7.14`` ``intel/2017b`` +``2.7.1`` ``foss/2018a``, ``foss/2018b``, ``intel/2018a``, ``intel/2018b`` +``2.7.1`` ``-Python-2.7.14`` ``intel/2017b`` +``2.8.1`` ``foss/2018b`` +``2.9.0`` ``gompi/2019a``, ``gompi/2019b``, ``iimpi/2019a``, ``iimpi/2019b`` +========== ================== ================================================================== .. _list_software_BLAT_291: @@ -2627,11 +2856,11 @@ BLAT on DNA is designed to quickly find sequences of 95% and greater similarity *homepage*: http://genome.ucsc.edu/FAQ/FAQblat.html -======= ====================================================================================== -version toolchain -======= ====================================================================================== -``3.5`` ``GCC/8.2.0-2.31.1``, ``foss/2016b``, ``foss/2018b``, ``intel/2016b``, ``intel/2017a`` -======= ====================================================================================== +======= ===================================================================================================== +version toolchain +======= ===================================================================================================== +``3.5`` ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0``, ``foss/2016b``, ``foss/2018b``, ``intel/2016b``, ``intel/2017a`` +======= ===================================================================================================== .. _list_software_Blender_700: @@ -2711,7 +2940,7 @@ version versionsuffix toolchain Blosc, an extremely fast, multi-threaded, meta-compressor library -*homepage*: http://www.blosc.org/ +*homepage*: https://www.blosc.org/ ========== ================================================================== version toolchain @@ -2721,6 +2950,7 @@ version toolchain ``1.14.2`` ``GCCcore/6.4.0``, ``foss/2016a`` ``1.14.4`` ``GCCcore/7.3.0`` ``1.17.0`` ``GCCcore/8.2.0`` +``1.17.1`` ``GCCcore/8.3.0`` ========== ================================================================== @@ -2781,16 +3011,16 @@ Statistical and novel interactive HTML plots for Python *homepage*: https://github.com/bokeh/bokeh -=========== ================== =============================== -version versionsuffix toolchain -=========== ================== =============================== -``0.12.3`` ``-Python-2.7.12`` ``intel/2016b`` -``0.12.3`` ``-Python-3.5.2`` ``intel/2016b`` -``0.12.15`` ``-Python-3.6.4`` ``intel/2018a`` -``1.0.4`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` -``1.3.4`` ``-Python-3.7.2`` ``foss/2019a`` -``1.4.0`` ``-Python-3.7.4`` ``foss/2019b`` -=========== ================== =============================== +=========== ================== ================================== +version versionsuffix toolchain +=========== ================== ================================== +``0.12.3`` ``-Python-2.7.12`` ``intel/2016b`` +``0.12.3`` ``-Python-3.5.2`` ``intel/2016b`` +``0.12.15`` ``-Python-3.6.4`` ``intel/2018a`` +``1.0.4`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` +``1.3.4`` ``-Python-3.7.2`` ``foss/2019a`` +``1.4.0`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` +=========== ================== ================================== .. _list_software_BoltzTraP_898: @@ -2809,6 +3039,22 @@ version toolchain ========= =============== +.. _list_software_Bonito_619: + +*Bonito* +++++++++ + +Convolution Basecaller for Oxford Nanopore Reads + +*homepage*: https://github.com/nanoporetech/bonito + +========= ================= ================================== +version versionsuffix toolchain +========= ================= ================================== +``0.1.0`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` +========= ================= ================================== + + .. _list_software_Bonmin_611: *Bonmin* @@ -2892,7 +3138,7 @@ version versionsuffix toolchain ``1.68.0`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` ``1.69.0`` ``intel/2019.01`` ``1.70.0`` ``gompi/2019a``, ``iimpi/2019a``, ``iimpic/2019a`` -``1.71.0`` ``gompi/2019b``, ``iimpi/2019b`` +``1.71.0`` ``gompi/2019b``, ``gompic/2019b``, ``iimpi/2019b`` ========== ================== ==================================================================== @@ -2944,14 +3190,14 @@ Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short DN *homepage*: http://bowtie-bio.sourceforge.net/index.shtml -=========== ======================================================================================================= -version toolchain -=========== ======================================================================================================= -``1.1.2`` ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``foss/2016a``, ``intel/2016b``, ``intel/2017a``, ``intel/2018a`` -``1.2.1.1`` ``foss/2016b``, ``intel/2017b`` -``1.2.2`` ``foss/2018b``, ``intel/2017b``, ``intel/2018a`` -``1.2.3`` ``GCC/8.2.0-2.31.1``, ``foss/2018b``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1`` -=========== ======================================================================================================= +=========== ====================================================================================================================== +version toolchain +=========== ====================================================================================================================== +``1.1.2`` ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``foss/2016a``, ``intel/2016b``, ``intel/2017a``, ``intel/2018a`` +``1.2.1.1`` ``foss/2016b``, ``intel/2017b`` +``1.2.2`` ``foss/2018b``, ``intel/2017b``, ``intel/2018a`` +``1.2.3`` ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0``, ``foss/2018b``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``iccifort/2019.5.281`` +=========== ====================================================================================================================== .. _list_software_Bowtie2_668: @@ -2963,19 +3209,19 @@ Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads *homepage*: http://bowtie-bio.sourceforge.net/bowtie2/index.shtml -=========== ============================================================== -version toolchain -=========== ============================================================== -``2.2.8`` ``foss/2016a`` -``2.2.9`` ``foss/2016a``, ``intel/2016b`` -``2.3.2`` ``foss/2016b``, ``foss/2017a``, ``intel/2017a`` -``2.3.3.1`` ``intel/2017b`` -``2.3.4`` ``intel/2017b`` -``2.3.4.1`` ``foss/2017b``, ``intel/2017b``, ``intel/2018a`` -``2.3.4.2`` ``foss/2018b``, ``intel/2018b`` -``2.3.4.3`` ``foss/2017b`` -``2.3.5.1`` ``GCC/8.2.0-2.31.1``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1`` -=========== ============================================================== +=========== ====================================================================================================== +version toolchain +=========== ====================================================================================================== +``2.2.8`` ``foss/2016a`` +``2.2.9`` ``foss/2016a``, ``intel/2016b`` +``2.3.2`` ``foss/2016b``, ``foss/2017a``, ``intel/2017a`` +``2.3.3.1`` ``intel/2017b`` +``2.3.4`` ``intel/2017b`` +``2.3.4.1`` ``foss/2017b``, ``intel/2017b``, ``intel/2018a`` +``2.3.4.2`` ``foss/2018b``, ``intel/2018b`` +``2.3.4.3`` ``foss/2017b`` +``2.3.5.1`` ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``iccifort/2019.5.281`` +=========== ====================================================================================================== .. _list_software_Bpipe_496: @@ -3107,6 +3353,38 @@ version versionsuffix toolchain ========= ================== ================== +.. _list_software_BSMAPz_493: + +*BSMAPz* +++++++++ + +Updated and optimized fork of BSMAP. BSMAPz is a short reads mapping program for bisulfite sequencing in DNA methylation study. + +*homepage*: https://github.com/zyndagj/BSMAPz + +========= ================== =============== +version versionsuffix toolchain +========= ================== =============== +``1.1.1`` ``-Python-2.7.16`` ``intel/2019b`` +========= ================== =============== + + +.. _list_software_BSseeker2_838: + +*BSseeker2* ++++++++++++ + +BS-Seeker2 is a seamless and versatile pipeline for accurately and fast mapping the bisulfite-treated reads. + +*homepage*: http://pellegrini-legacy.mcdb.ucla.edu/bs_seeker2 + +========= ================== ====================================== +version versionsuffix toolchain +========= ================== ====================================== +``2.1.8`` ``-Python-2.7.16`` ``GCC/8.3.0``, ``iccifort/2019.5.281`` +========= ================== ====================================== + + .. _list_software_buildenv_857: *buildenv* @@ -3146,7 +3424,7 @@ version toolchain BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs -*homepage*: http://busco.ezlab.org/ +*homepage*: https://busco.ezlab.org/ ========= ================== =============== version versionsuffix toolchain @@ -3154,9 +3432,26 @@ version versionsuffix toolchain ``1.22`` ``-Python-2.7.13`` ``intel/2017a`` ``2.0.1`` ``-Python-2.7.13`` ``intel/2017a`` ``3.0.2`` ``-Python-2.7.15`` ``intel/2018b`` +``4.0.5`` ``-Python-3.7.4`` ``foss/2019b`` ========= ================== =============== +.. _list_software_BUStools_795: + +*BUStools* +++++++++++ + +bustools is a program for manipulating BUS files for single cell RNA-Seq datasets. It can be used to error correct barcodes, collapse UMIs, produce gene count or transcript compatibility count matrices, and is useful for many other tasks. See the kallisto | bustools website for examples and instructions on how to use bustools as part of a single-cell RNA-seq workflow. + +*homepage*: https://github.com/BUStools/bustools + +========== ============== +version toolchain +========== ============== +``0.40.0`` ``foss/2018b`` +========== ============== + + .. _list_software_BWA_218: *BWA* @@ -3166,15 +3461,15 @@ Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively sh *homepage*: http://bio-bwa.sourceforge.net/ -=========== ================================================================================================================================================================= -version toolchain -=========== ================================================================================================================================================================= -``0.7.12`` ``foss/2016b`` -``0.7.13`` ``foss/2016a``, ``intel/2016a`` -``0.7.15`` ``GCCcore/5.4.0``, ``GCCcore/6.4.0``, ``foss/2016a``, ``foss/2016b``, ``intel/2016b``, ``intel/2017a`` -``0.7.16a`` ``foss/2016b``, ``intel/2017a`` -``0.7.17`` ``GCC/8.2.0-2.31.1``, ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b`` -=========== ================================================================================================================================================================= +=========== ========================================================================================================================================================================================================= +version toolchain +=========== ========================================================================================================================================================================================================= +``0.7.12`` ``foss/2016b`` +``0.7.13`` ``foss/2016a``, ``intel/2016a`` +``0.7.15`` ``GCCcore/5.4.0``, ``GCCcore/6.4.0``, ``foss/2016a``, ``foss/2016b``, ``intel/2016b``, ``intel/2017a`` +``0.7.16a`` ``foss/2016b``, ``intel/2017a`` +``0.7.17`` ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0``, ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``iccifort/2019.5.281``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b`` +=========== ========================================================================================================================================================================================================= .. _list_software_bwa-meth_789: @@ -3186,11 +3481,11 @@ Fast and accurante alignment of BS-Seq reads. *homepage*: https://github.com/brentp/bwa-meth -========= ======================================== -version toolchain -========= ======================================== -``0.2.2`` ``iccifort/2019.1.144-GCC-8.2.0-2.31.1`` -========= ======================================== +========= ================================================================= +version toolchain +========= ================================================================= +``0.2.2`` ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``iccifort/2019.5.281`` +========= ================================================================= .. _list_software_bwakit_642: @@ -3222,6 +3517,7 @@ The BWidget Toolkit is a high-level Widget Set for Tcl/Tk built using native Tcl version toolchain ========== ================= ``1.9.13`` ``GCCcore/8.2.0`` +``1.9.14`` ``GCCcore/8.3.0`` ========== ================= @@ -3318,7 +3614,7 @@ version toolchain --- -:ref:`list_software_C3D_186` - :ref:`list_software_cadaver_726` - :ref:`list_software_Caffe_469` - :ref:`list_software_cairo_526` - :ref:`list_software_cairomm_744` - :ref:`list_software_Calendrical_1106` - :ref:`list_software_Cantera_702` - :ref:`list_software_canu_423` - :ref:`list_software_Canvas_604` - :ref:`list_software_CAP3_263` - :ref:`list_software_CapnProto_918` - :ref:`list_software_Cargo_492` - :ref:`list_software_CastXML_636` - :ref:`list_software_Catch2_533` - :ref:`list_software_CatMAP_502` - :ref:`list_software_causalml_850` - :ref:`list_software_CaVEMan_603` - :ref:`list_software_CBLAS_357` - :ref:`list_software_ccache_599` - :ref:`list_software_CCL_210` - :ref:`list_software_cclib_509` - :ref:`list_software_CD-HIT_409` - :ref:`list_software_cDNA_Cupcake_1105` - :ref:`list_software_CDO_214` - :ref:`list_software_cdsapi_628` - :ref:`list_software_CellMix_686` - :ref:`list_software_CellRanger_991` - :ref:`list_software_Centrifuge_1036` - :ref:`list_software_CESM-deps_769` - :ref:`list_software_CFITSIO_529` - :ref:`list_software_cftime_632` - :ref:`list_software_CGAL_279` - :ref:`list_software_cget_419` - :ref:`list_software_CGNS_299` - :ref:`list_software_CharLS_541` - :ref:`list_software_charmm_632` - :ref:`list_software_CHARMM_440` - :ref:`list_software_CHASE_356` - :ref:`list_software_CheckM_555` - :ref:`list_software_Cheetah_690` - :ref:`list_software_CheMPS2_562` - :ref:`list_software_Chimera_697` - :ref:`list_software_ChimPipe_783` - :ref:`list_software_Chromaprint_1159` - :ref:`list_software_CIRCexplorer_1170` - :ref:`list_software_CIRCexplorer2_1220` - :ref:`list_software_Circos_611` - :ref:`list_software_CIRI_295` - :ref:`list_software_cisTEM_549` - :ref:`list_software_CITE-seq-Count_1233` - :ref:`list_software_Clang_485` - :ref:`list_software_Clang-Python-bindings_2063` - :ref:`list_software_CLAPACK_495` - :ref:`list_software_CLHEP_364` - :ref:`list_software_CLISP_379` - :ref:`list_software_ClonalFrameML_1245` - :ref:`list_software_CLooG_436` - :ref:`list_software_Clustal-Omega_1262` - :ref:`list_software_ClustalW2_865` - :ref:`list_software_Cluster-Buster_1412` - :ref:`list_software_ClusterShell_1242` - :ref:`list_software_CMake_449` - :ref:`list_software_CNT-ILP_503` - :ref:`list_software_CNVkit_559` - :ref:`list_software_CNVnator_779` - :ref:`list_software_CODEX2_421` - :ref:`list_software_Commet_613` - :ref:`list_software_Con3F_409` - :ref:`list_software_CONCOCT_521` - :ref:`list_software_configparser_1283` - :ref:`list_software_configurable-http-proxy_2381` - :ref:`list_software_ConnectomeWorkbench_1966` - :ref:`list_software_Control-FREEC_1139` - :ref:`list_software_CoordgenLibs_1211` - :ref:`list_software_Coot_405` - :ref:`list_software_core-counter_1238` - :ref:`list_software_Coreutils_954` - :ref:`list_software_corner_649` - :ref:`list_software_coverage_844` - :ref:`list_software_cowsay_662` - :ref:`list_software_CP2K_272` - :ref:`list_software_CPB_213` - :ref:`list_software_CPLEX_380` - :ref:`list_software_CppUnit_707` - :ref:`list_software_cram_419` - :ref:`list_software_cramtools_980` - :ref:`list_software_CrayCCE_602` - :ref:`list_software_CrayGNU_633` - :ref:`list_software_CrayIntel_907` - :ref:`list_software_CrayPGI_623` - :ref:`list_software_crb-blast_890` - :ref:`list_software_CRF++_305` - :ref:`list_software_CrossMap_808` - :ref:`list_software_CrossTalkZ_1008` - :ref:`list_software_CRPropa_663` - :ref:`list_software_CryptoMiniSat_1334` - :ref:`list_software_CSBDeep_598` - :ref:`list_software_cscope_637` - :ref:`list_software_csvkit_660` - :ref:`list_software_ctags_530` - :ref:`list_software_ctffind_734` - :ref:`list_software_Cube_383` - :ref:`list_software_CubeGUI_612` - :ref:`list_software_CubeLib_662` - :ref:`list_software_CubeWriter_1020` - :ref:`list_software_CUDA_285` - :ref:`list_software_cuDNN_440` - :ref:`list_software_Cufflinks_933` - :ref:`list_software_CUnit_483` - :ref:`list_software_cURL_342` - :ref:`list_software_custodian_970` - :ref:`list_software_cutadapt_854` - :ref:`list_software_CVS_236` - :ref:`list_software_CVXOPT_484` - :ref:`list_software_CVXPY_410` - :ref:`list_software_cysignals_973` - :ref:`list_software_Cython_629` - :ref:`list_software_cytoolz_788` - :ref:`list_software_cytosim_776` - :ref:`list_software_cyvcf2_589` +:ref:`list_software_C3D_186` - :ref:`list_software_cadaver_726` - :ref:`list_software_Caffe_469` - :ref:`list_software_cairo_526` - :ref:`list_software_cairomm_744` - :ref:`list_software_Calendrical_1106` - :ref:`list_software_Cantera_702` - :ref:`list_software_canu_423` - :ref:`list_software_Canvas_604` - :ref:`list_software_CAP3_263` - :ref:`list_software_CapnProto_918` - :ref:`list_software_Cargo_492` - :ref:`list_software_CastXML_636` - :ref:`list_software_Catch2_533` - :ref:`list_software_CatMAP_502` - :ref:`list_software_causalml_850` - :ref:`list_software_CaVEMan_603` - :ref:`list_software_Cbc_264` - :ref:`list_software_CBLAS_357` - :ref:`list_software_ccache_599` - :ref:`list_software_CCL_210` - :ref:`list_software_cclib_509` - :ref:`list_software_CD-HIT_409` - :ref:`list_software_cDNA_Cupcake_1105` - :ref:`list_software_CDO_214` - :ref:`list_software_cdsapi_628` - :ref:`list_software_CellMix_686` - :ref:`list_software_CellRanger_991` - :ref:`list_software_Centrifuge_1036` - :ref:`list_software_CESM-deps_769` - :ref:`list_software_CFITSIO_529` - :ref:`list_software_cftime_632` - :ref:`list_software_CGAL_279` - :ref:`list_software_cget_419` - :ref:`list_software_Cgl_278` - :ref:`list_software_CGmapTools_985` - :ref:`list_software_CGNS_299` - :ref:`list_software_CharLS_541` - :ref:`list_software_charmm_632` - :ref:`list_software_CHARMM_440` - :ref:`list_software_CHASE_356` - :ref:`list_software_CheckM_555` - :ref:`list_software_Cheetah_690` - :ref:`list_software_CheMPS2_562` - :ref:`list_software_Chimera_697` - :ref:`list_software_ChimPipe_783` - :ref:`list_software_Chromaprint_1159` - :ref:`list_software_CIRCexplorer_1170` - :ref:`list_software_CIRCexplorer2_1220` - :ref:`list_software_Circos_611` - :ref:`list_software_CIRI_295` - :ref:`list_software_cisTEM_549` - :ref:`list_software_CITE-seq-Count_1233` - :ref:`list_software_Clang_485` - :ref:`list_software_Clang-Python-bindings_2063` - :ref:`list_software_CLAPACK_495` - :ref:`list_software_CLHEP_364` - :ref:`list_software_CLISP_379` - :ref:`list_software_ClonalFrameML_1245` - :ref:`list_software_CLooG_436` - :ref:`list_software_Clp_287` - :ref:`list_software_Clustal-Omega_1262` - :ref:`list_software_ClustalW2_865` - :ref:`list_software_Cluster-Buster_1412` - :ref:`list_software_ClusterShell_1242` - :ref:`list_software_CMake_449` - :ref:`list_software_CNT-ILP_503` - :ref:`list_software_CNVkit_559` - :ref:`list_software_CNVnator_779` - :ref:`list_software_CODEX2_421` - :ref:`list_software_CoinUtils_922` - :ref:`list_software_Commet_613` - :ref:`list_software_Con3F_409` - :ref:`list_software_CONCOCT_521` - :ref:`list_software_configparser_1283` - :ref:`list_software_configurable-http-proxy_2381` - :ref:`list_software_ConnectomeWorkbench_1966` - :ref:`list_software_Control-FREEC_1139` - :ref:`list_software_CoordgenLibs_1211` - :ref:`list_software_Coot_405` - :ref:`list_software_core-counter_1238` - :ref:`list_software_Coreutils_954` - :ref:`list_software_corner_649` - :ref:`list_software_coverage_844` - :ref:`list_software_cowsay_662` - :ref:`list_software_CP2K_272` - :ref:`list_software_CPB_213` - :ref:`list_software_CPLEX_380` - :ref:`list_software_CppUnit_707` - :ref:`list_software_cram_419` - :ref:`list_software_cramtools_980` - :ref:`list_software_CrayCCE_602` - :ref:`list_software_CrayGNU_633` - :ref:`list_software_CrayIntel_907` - :ref:`list_software_CrayPGI_623` - :ref:`list_software_crb-blast_890` - :ref:`list_software_CRF++_305` - :ref:`list_software_CrossMap_808` - :ref:`list_software_CrossTalkZ_1008` - :ref:`list_software_CRPropa_663` - :ref:`list_software_CryptoMiniSat_1334` - :ref:`list_software_CSBDeep_598` - :ref:`list_software_cscope_637` - :ref:`list_software_csvkit_660` - :ref:`list_software_ctags_530` - :ref:`list_software_ctffind_734` - :ref:`list_software_Cube_383` - :ref:`list_software_CubeGUI_612` - :ref:`list_software_CubeLib_662` - :ref:`list_software_CubeWriter_1020` - :ref:`list_software_CUDA_285` - :ref:`list_software_cuDNN_440` - :ref:`list_software_Cufflinks_933` - :ref:`list_software_CUnit_483` - :ref:`list_software_cURL_342` - :ref:`list_software_custodian_970` - :ref:`list_software_cutadapt_854` - :ref:`list_software_CVS_236` - :ref:`list_software_CVXOPT_484` - :ref:`list_software_CVXPY_410` - :ref:`list_software_cysignals_973` - :ref:`list_software_Cython_629` - :ref:`list_software_cytoolz_788` - :ref:`list_software_cytosim_776` - :ref:`list_software_cyvcf2_589` .. _list_software_C3D_186: @@ -3454,7 +3750,7 @@ version versionsuffix toolchain Canu is a fork of the Celera Assembler designed for high-noise single-molecule sequencing -*homepage*: http://canu.readthedocs.io +*homepage*: https://canu.readthedocs.io ======= ================ =============================== version versionsuffix toolchain @@ -3464,6 +3760,7 @@ version versionsuffix toolchain ``1.8`` ``-Perl-5.26.0`` ``foss/2017b``, ``intel/2017b`` ``1.8`` ``-Perl-5.28.0`` ``foss/2018b`` ``1.8`` ``-Perl-5.28.1`` ``GCCcore/8.2.0`` +``1.9`` ``-Java-11`` ``GCCcore/8.3.0`` ======= ================ =============================== @@ -3616,6 +3913,22 @@ version toolchain ========== ============== +.. _list_software_Cbc_264: + +*Cbc* ++++++ + +Cbc (Coin-or branch and cut) is an open-source mixed integer linear programming solver written in C++. It can be used as a callable library or using a stand-alone executable. + +*homepage*: https://github.com/coin-or/Cbc + +========== ============== +version toolchain +========== ============== +``2.10.3`` ``foss/2018b`` +========== ============== + + .. _list_software_CBLAS_357: *CBLAS* @@ -3887,7 +4200,7 @@ version versionsuffix toolchain ``4.11.1`` ``-Python-3.6.4`` ``foss/2018a`` ``4.11.1`` ``-Python-3.6.6`` ``foss/2018b`` ``4.14`` ``-Python-3.7.2`` ``foss/2019a``, ``intel/2019a`` -``4.14.1`` ``-Python-3.7.4`` ``foss/2019b`` +``4.14.1`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` ========== ================== =============================== @@ -3907,6 +4220,38 @@ version versionsuffix toolchain ========= ================= ============== +.. _list_software_Cgl_278: + +*Cgl* ++++++ + +The COIN-OR Cut Generation Library (Cgl) is a collection of cut generators that can be used with other COIN-OR packages that make use of cuts, such as, among others, the linear solver Clp or the mixed integer linear programming solvers Cbc or BCP. Cgl uses the abstract class OsiSolverInterface (see Osi) to use or communicate with a solver. It does not directly call a solver. + +*homepage*: https://github.com/coin-or/Cgl + +========== ============== +version toolchain +========== ============== +``0.60.2`` ``foss/2018b`` +========== ============== + + +.. _list_software_CGmapTools_985: + +*CGmapTools* +++++++++++++ + +Command-line Toolset for Bisulfite Sequencing Data Analysis + +*homepage*: https://cgmaptools.github.io/ + +========= =============== +version toolchain +========= =============== +``0.1.2`` ``intel/2019b`` +========= =============== + + .. _list_software_CGNS_299: *CGNS* @@ -3936,6 +4281,7 @@ CharLS is a C++ implementation of the JPEG-LS standard for lossless and near-los version toolchain ========= ==================================== ``2.0.0`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` +``2.1.0`` ``GCCcore/8.2.0`` ========= ==================================== @@ -4003,6 +4349,7 @@ version versionsuffix toolchain ``1.0.13`` ``-Python-2.7.15`` ``foss/2018b`` ``1.0.13`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` ``1.0.18`` ``-Python-2.7.15`` ``foss/2019a`` +``1.1.2`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` ========== ================== =============================== @@ -4201,29 +4548,30 @@ C, C++, Objective-C compiler, based on LLVM. Does not include C++ standard lib *homepage*: https://clang.llvm.org/ -========= ================== ====================================== -version versionsuffix toolchain -========= ================== ====================================== -``3.3`` ``GCC/4.8.1`` -``3.4`` ``GCC/4.8.2`` -``3.4.1`` ``GCC/4.8.2`` -``3.4.2`` ``GCC/4.8.2`` -``3.6.0`` ``GCC/4.9.2`` -``3.6.1`` ``GCC/4.9.2`` -``3.7.0`` ``GNU/4.9.3-2.25`` -``3.7.1`` ``GCC/4.9.3-2.25``, ``foss/2016a`` -``3.8.0`` ``GCC/4.9.3-2.25`` -``3.8.1`` ``GCC/5.4.0-2.26``, ``foss/2016b`` -``5.0.0`` ``GCC/6.4.0-2.28`` -``5.0.1`` ``GCC/6.4.0-2.28`` -``6.0.1`` ``GCC/6.4.0-2.28``, ``GCC/7.3.0-2.30`` -``7.0.0`` ``GCC/6.4.0-2.28`` -``7.0.1`` ``GCC/7.3.0-2.30`` -``8.0.0`` ``GCCcore/8.2.0`` -``8.0.0`` ``-CUDA-10.1.105`` ``GCCcore/8.2.0`` -``9.0.1`` ``GCCcore/8.3.0`` -``9.0.1`` ``-CUDA-10.1.243`` ``GCC/8.3.0`` -========= ================== ====================================== +========== ================== ====================================== +version versionsuffix toolchain +========== ================== ====================================== +``3.3`` ``GCC/4.8.1`` +``3.4`` ``GCC/4.8.2`` +``3.4.1`` ``GCC/4.8.2`` +``3.4.2`` ``GCC/4.8.2`` +``3.6.0`` ``GCC/4.9.2`` +``3.6.1`` ``GCC/4.9.2`` +``3.7.0`` ``GNU/4.9.3-2.25`` +``3.7.1`` ``GCC/4.9.3-2.25``, ``foss/2016a`` +``3.8.0`` ``GCC/4.9.3-2.25`` +``3.8.1`` ``GCC/5.4.0-2.26``, ``foss/2016b`` +``5.0.0`` ``GCC/6.4.0-2.28`` +``5.0.1`` ``GCC/6.4.0-2.28`` +``6.0.1`` ``GCC/6.4.0-2.28``, ``GCC/7.3.0-2.30`` +``7.0.0`` ``GCC/6.4.0-2.28`` +``7.0.1`` ``GCC/7.3.0-2.30`` +``8.0.0`` ``GCCcore/8.2.0`` +``8.0.0`` ``-CUDA-10.1.105`` ``GCCcore/8.2.0`` +``9.0.1`` ``GCCcore/8.3.0`` +``9.0.1`` ``-CUDA-10.1.243`` ``GCC/8.3.0`` +``10.0.0`` ``GCCcore/8.3.0`` +========== ================== ====================================== .. _list_software_Clang-Python-bindings_2063: @@ -4328,6 +4676,22 @@ version toolchain ========== ============= +.. _list_software_Clp_287: + +*Clp* ++++++ + +Clp (Coin-or linear programming) is an open-source linear programming solver. It is primarily meant to be used as a callable library, but a basic, stand-alone executable version is also available. + +*homepage*: https://github.com/coin-or/Clp + +========== ============== +version toolchain +========== ============== +``1.17.3`` ``foss/2018b`` +========== ============== + + .. _list_software_Clustal-Omega_1262: *Clustal-Omega* @@ -4337,12 +4701,12 @@ Clustal Omega is a multiple sequence alignment program for proteins. It produce *homepage*: http://www.clustal.org/omega/ -========= ================================================ -version toolchain -========= ================================================ -``1.2.0`` ``foss/2016b`` -``1.2.4`` ``foss/2018b``, ``intel/2018a``, ``intel/2018b`` -========= ================================================ +========= =============================================================== +version toolchain +========= =============================================================== +``1.2.0`` ``foss/2016b`` +``1.2.4`` ``GCC/8.3.0``, ``foss/2018b``, ``intel/2018a``, ``intel/2018b`` +========= =============================================================== .. _list_software_ClustalW2_865: @@ -4505,6 +4869,22 @@ version versionsuffix toolchain ============ ============= =============== +.. _list_software_CoinUtils_922: + +*CoinUtils* ++++++++++++ + +CoinUtils (Coin-OR Utilities) is an open-source collection of classes and functions that are generally useful to more than one COIN-OR project. + +*homepage*: https://github.com/coin-or/CoinUtils + +========== ================= +version toolchain +========== ================= +``2.11.3`` ``GCCcore/7.3.0`` +========== ================= + + .. _list_software_Commet_613: *Commet* @@ -4798,14 +5178,15 @@ version toolchain *CppUnit* +++++++++ -CppUnit is the C++ port of the famous JUnit framework for unit testing. +CppUnit is the C++ port of the famous JUnit framework for unit testing. -*homepage*: http://sourceforge.net/projects/cppunit/ +*homepage*: https://freedesktop.org/wiki/Software/cppunit/ ========== ==================================================== version toolchain ========== ==================================================== ``1.12.1`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``foss/2016a`` +``1.15.1`` ``GCCcore/8.3.0`` ========== ==================================================== @@ -4915,11 +5296,12 @@ Conditional Reciprocal Best BLAST - high confidence ortholog assignment. CRB-BL *homepage*: https://github.com/cboursnell/crb-blast -========= =============== -version toolchain -========= =============== -``0.6.9`` ``intel/2017a`` -========= =============== +========= =============== =============== +version versionsuffix toolchain +========= =============== =============== +``0.6.9`` ``intel/2017a`` +``0.6.9`` ``-Ruby-2.6.1`` ``foss/2018b`` +========= =============== =============== .. _list_software_CRF++_305: @@ -5295,7 +5677,7 @@ version versionsuffix toolchain Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads. -*homepage*: http://opensource.scilifelab.se/projects/cutadapt/ +*homepage*: https://opensource.scilifelab.se/projects/cutadapt/ ========= ================== ================================================ version versionsuffix toolchain @@ -5307,10 +5689,12 @@ version versionsuffix toolchain ``1.16`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b``, ``intel/2018a`` ``1.16`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` ``1.16`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` -``1.18`` ``GCCcore/8.2.0`` +``1.18`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` ``1.18`` ``-Python-2.7.15`` ``foss/2018b`` ``1.18`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` ``2.1`` ``-Python-3.6.6`` ``foss/2018b`` +``2.7`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` +``2.8`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` ========= ================== ================================================ @@ -5357,11 +5741,12 @@ CVXPY is a Python-embedded modeling language for convex optimization problems. *homepage*: https://www.cvxpy.org/ -========== ============== -version toolchain -========== ============== -``1.0.24`` ``foss/2019a`` -========== ============== +========== ================= ============== +version versionsuffix toolchain +========== ================= ============== +``1.0.24`` ``foss/2019a`` +``1.0.28`` ``-Python-3.7.4`` ``foss/2019b`` +========== ================= ============== .. _list_software_cysignals_973: @@ -5458,7 +5843,7 @@ version versionsuffix toolchain --- -:ref:`list_software_dadi_402` - :ref:`list_software_dagitty_758` - :ref:`list_software_damageproto_1171` - :ref:`list_software_dammit_636` - :ref:`list_software_DANPOS2_503` - :ref:`list_software_DAS_Tool_725` - :ref:`list_software_dask_419` - :ref:`list_software_datamash_835` - :ref:`list_software_davix_540` - :ref:`list_software_DB_134` - :ref:`list_software_DB_File_613` - :ref:`list_software_DBD-mysql_813` - :ref:`list_software_DBG2OLC_477` - :ref:`list_software_DBus_366` - :ref:`list_software_dbus-glib_889` - :ref:`list_software_dcm2niix_798` - :ref:`list_software_DCMTK_371` - :ref:`list_software_deal.II_598` - :ref:`list_software_deap_410` - :ref:`list_software_deconf_623` - :ref:`list_software_DeconICA_694` - :ref:`list_software_deepdiff_823` - :ref:`list_software_DeepSurv_814` - :ref:`list_software_deepTools_943` - :ref:`list_software_Delly_506` - :ref:`list_software_DeMixT_555` - :ref:`list_software_DendroPy_805` - :ref:`list_software_destiny_768` - :ref:`list_software_detonate_852` - :ref:`list_software_DFT-D3_386` - :ref:`list_software_DFTB+_331` - :ref:`list_software_DIAL_282` - :ref:`list_software_DIAMOND_508` - :ref:`list_software_DicomBrowser_1232` - :ref:`list_software_Diffutils_938` - :ref:`list_software_dill_421` - :ref:`list_software_distributed_1187` - :ref:`list_software_DL_POLY_Classic_1364` - :ref:`list_software_DMTCP_376` - :ref:`list_software_DOLFIN_444` - :ref:`list_software_Doris_513` - :ref:`list_software_dotNET-Core-Runtime_1781` - :ref:`list_software_double-conversion_1774` - :ref:`list_software_Doxygen_734` - :ref:`list_software_Drake_487` - :ref:`list_software_dropEst_737` - :ref:`list_software_DSA_216` - :ref:`list_software_DSRC_300` - :ref:`list_software_Dsuite_622` - :ref:`list_software_dtcmp_536` - :ref:`list_software_dxpy_453` +:ref:`list_software_dadi_402` - :ref:`list_software_dagitty_758` - :ref:`list_software_damageproto_1171` - :ref:`list_software_dammit_636` - :ref:`list_software_DANPOS2_503` - :ref:`list_software_DAS_Tool_725` - :ref:`list_software_dask_419` - :ref:`list_software_datamash_835` - :ref:`list_software_davix_540` - :ref:`list_software_DB_134` - :ref:`list_software_DB_File_613` - :ref:`list_software_DBD-mysql_813` - :ref:`list_software_DBG2OLC_477` - :ref:`list_software_DBus_366` - :ref:`list_software_dbus-glib_889` - :ref:`list_software_dcm2niix_798` - :ref:`list_software_DCMTK_371` - :ref:`list_software_deal.II_598` - :ref:`list_software_deap_410` - :ref:`list_software_deconf_623` - :ref:`list_software_DeconICA_694` - :ref:`list_software_deepdiff_823` - :ref:`list_software_DeepSurv_814` - :ref:`list_software_deepTools_943` - :ref:`list_software_Delly_506` - :ref:`list_software_DeMixT_555` - :ref:`list_software_DendroPy_805` - :ref:`list_software_destiny_768` - :ref:`list_software_detonate_852` - :ref:`list_software_DFT-D3_386` - :ref:`list_software_DFTB+_331` - :ref:`list_software_DIAL_282` - :ref:`list_software_DIAMOND_508` - :ref:`list_software_DicomBrowser_1232` - :ref:`list_software_Diffutils_938` - :ref:`list_software_dill_421` - :ref:`list_software_distributed_1187` - :ref:`list_software_DL_POLY_Classic_1364` - :ref:`list_software_DMTCP_376` - :ref:`list_software_DOLFIN_444` - :ref:`list_software_Doris_513` - :ref:`list_software_dotNET-Core-Runtime_1781` - :ref:`list_software_double-conversion_1774` - :ref:`list_software_Doxygen_734` - :ref:`list_software_Drake_487` - :ref:`list_software_dropEst_737` - :ref:`list_software_DSA_216` - :ref:`list_software_DSRC_300` - :ref:`list_software_Dsuite_622` - :ref:`list_software_dtcmp_536` - :ref:`list_software_dtcwt_550` - :ref:`list_software_dxpy_453` .. _list_software_dadi_402: @@ -5585,7 +5970,7 @@ version versionsuffix toolchain ``1.0.0`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` ``1.1.4`` ``-Python-2.7.15`` ``fosscuda/2018b`` ``2.3.0`` ``-Python-3.7.2`` ``foss/2019a`` -``2.8.0`` ``-Python-3.7.4`` ``foss/2019b`` +``2.8.0`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` ========== ================== =================================================== @@ -5612,13 +5997,14 @@ version toolchain The davix project aims to make file management over HTTP-based protocols simple. The focus is on high-performance remote I/O and data management of large collections of files. Currently, there is support for the WebDav (link is external), Amazon S3 (link is external), Microsoft Azure (link is external), and HTTP (link is external) protocols. -*homepage*: http://dmc.web.cern.ch/projects/davix/home +*homepage*: https://dmc.web.cern.ch/projects/davix/home -========= =============== -version toolchain -========= =============== -``0.6.6`` ``intel/2017a`` -========= =============== +========= ================= +version toolchain +========= ================= +``0.6.6`` ``intel/2017a`` +``0.7.5`` ``GCCcore/8.3.0`` +========= ================= .. _list_software_DB_134: @@ -5630,15 +6016,15 @@ Berkeley DB enables the development of custom data management solutions, withou *homepage*: http://www.oracle.com/technetwork/products/berkeleydb -=========== ================================== -version toolchain -=========== ================================== -``4.8.30`` ``intel/2016a`` -``6.2.23`` ``foss/2016a`` -``6.2.32`` ``GCCcore/6.4.0``, ``intel/2017a`` -``18.1.25`` ``GCCcore/7.3.0`` -``18.1.32`` ``GCCcore/8.2.0`` -=========== ================================== +=========== ==================================== +version toolchain +=========== ==================================== +``4.8.30`` ``intel/2016a`` +``6.2.23`` ``foss/2016a`` +``6.2.32`` ``GCCcore/6.4.0``, ``intel/2017a`` +``18.1.25`` ``GCCcore/7.3.0`` +``18.1.32`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` +=========== ==================================== .. _list_software_DB_File_613: @@ -5751,7 +6137,7 @@ dcm2niix is a designed to convert neuroimaging data from the DICOM format to the version toolchain ================ ==================================== ``1.0.20180622`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` -``1.0.20190902`` ``GCCcore/7.3.0`` +``1.0.20190902`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` ================ ==================================== @@ -5929,12 +6315,12 @@ A Python library for phylogenetics and phylogenetic computing: reading, writing *homepage*: https://pypi.python.org/pypi/DendroPy/ -========= ================== ================================== -version versionsuffix toolchain -========= ================== ================================== -``4.4.0`` ``GCCcore/8.2.0``, ``intel/2019a`` -``4.4.0`` ``-Python-2.7.15`` ``intel/2018b`` -========= ================== ================================== +========= ================== ===================================================== +version versionsuffix toolchain +========= ================== ===================================================== +``4.4.0`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``intel/2019a`` +``4.4.0`` ``-Python-2.7.15`` ``intel/2018b`` +========= ================== ===================================================== .. _list_software_destiny_768: @@ -5978,11 +6364,11 @@ DFT-D3 implements a dispersion correction for density functionals, Hartree-Fock *homepage*: http://www.thch.uni-bonn.de/tc/index.php?section=downloads&subsection=DFT-D3&lang=english -========= =============== -version toolchain -========= =============== -``3.2.0`` ``intel/2019a`` -========= =============== +========= ============================== +version toolchain +========= ============================== +``3.2.0`` ``GCC/8.3.0``, ``intel/2019a`` +========= ============================== .. _list_software_DFTB+_331: @@ -6032,6 +6418,7 @@ version toolchain ========== ================================================================ ``0.9.22`` ``foss/2018a``, ``foss/2018b``, ``intel/2018a``, ``intel/2018b`` ``0.9.24`` ``iccifort/2019.1.144-GCC-8.2.0-2.31.1`` +``0.9.30`` ``GCC/8.3.0``, ``iccifort/2019.5.281`` ========== ================================================================ @@ -6323,6 +6710,23 @@ version toolchain ========= ================================ +.. _list_software_dtcwt_550: + +*dtcwt* ++++++++ + +Dual-Tree Complex Wavelet Transform library for Python + +*homepage*: https://github.com/rjw57/dtcwt + +========== ================== =============== +version versionsuffix toolchain +========== ================== =============== +``0.12.0`` ``-Python-2.7.15`` ``foss/2018b`` +``0.12.0`` ``-Python-3.7.4`` ``intel/2019b`` +========== ================== =============== + + .. _list_software_dxpy_453: *dxpy* @@ -6345,7 +6749,7 @@ version versionsuffix toolchain --- -:ref:`list_software_ea-utils_804` - :ref:`list_software_earthengine-api_1521` - :ref:`list_software_EasyBuild_898` - :ref:`list_software_EasyQC_550` - :ref:`list_software_ecCodes_694` - :ref:`list_software_ED2_187` - :ref:`list_software_EggLib_554` - :ref:`list_software_eggnog-mapper_1321` - :ref:`list_software_Eigen_488` - :ref:`list_software_EIGENSOFT_676` - :ref:`list_software_elastix_762` - :ref:`list_software_Elk_284` - :ref:`list_software_ELPA_290` - :ref:`list_software_ELPH_297` - :ref:`list_software_Emacs_489` - :ref:`list_software_EMAN2_339` - :ref:`list_software_EMBOSS_457` - :ref:`list_software_emcee_511` - :ref:`list_software_enaBrowserTool_1462` - :ref:`list_software_enchant_737` - :ref:`list_software_entrypoints_1231` - :ref:`list_software_EPD_217` - :ref:`list_software_EPIC_289` - :ref:`list_software_EricScript_1016` - :ref:`list_software_ESMF_299` - :ref:`list_software_Essentia_828` - :ref:`list_software_ETE_222` - :ref:`list_software_ETSF_IO_553` - :ref:`list_software_eudev_537` - :ref:`list_software_EvidentialGene_1412` - :ref:`list_software_evmix_553` - :ref:`list_software_ExaBayes_786` - :ref:`list_software_Exonerate_939` - :ref:`list_software_expat_546` - :ref:`list_software_expect_649` - :ref:`list_software_eXpress_746` - :ref:`list_software_Extrae_617` +:ref:`list_software_ea-utils_804` - :ref:`list_software_earthengine-api_1521` - :ref:`list_software_EasyBuild_898` - :ref:`list_software_EasyQC_550` - :ref:`list_software_ecCodes_694` - :ref:`list_software_ED2_187` - :ref:`list_software_EggLib_554` - :ref:`list_software_eggnog-mapper_1321` - :ref:`list_software_Eigen_488` - :ref:`list_software_EIGENSOFT_676` - :ref:`list_software_elastix_762` - :ref:`list_software_Elk_284` - :ref:`list_software_ELPA_290` - :ref:`list_software_ELPH_297` - :ref:`list_software_ELSI_301` - :ref:`list_software_Emacs_489` - :ref:`list_software_EMAN2_339` - :ref:`list_software_EMBOSS_457` - :ref:`list_software_emcee_511` - :ref:`list_software_enaBrowserTool_1462` - :ref:`list_software_enchant_737` - :ref:`list_software_EnsEMBLCoreAPI_1193` - :ref:`list_software_entrypoints_1231` - :ref:`list_software_EPD_217` - :ref:`list_software_EPIC_289` - :ref:`list_software_EricScript_1016` - :ref:`list_software_ESMF_299` - :ref:`list_software_Essentia_828` - :ref:`list_software_ETE_222` - :ref:`list_software_ETSF_IO_553` - :ref:`list_software_eudev_537` - :ref:`list_software_EvidentialGene_1412` - :ref:`list_software_evmix_553` - :ref:`list_software_ExaBayes_786` - :ref:`list_software_Exonerate_939` - :ref:`list_software_expat_546` - :ref:`list_software_expect_649` - :ref:`list_software_eXpress_746` - :ref:`list_software_Extrae_617` .. _list_software_ea-utils_804: @@ -6463,6 +6867,8 @@ version toolchain ``4.0.0`` ``system`` ``4.0.1`` ``system`` ``4.1.0`` ``system`` +``4.1.1`` ``system`` +``4.1.2`` ``system`` ========== ========== @@ -6637,7 +7043,7 @@ version toolchain Eigenvalue SoLvers for Petaflop-Applications . -*homepage*: http://elpa.rzg.mpg.de +*homepage*: https://elpa.rzg.mpg.de =================== ================================================ version toolchain @@ -6648,6 +7054,7 @@ version toolchain ``2017.11.001`` ``foss/2018b``, ``intel/2018a``, ``intel/2018b`` ``2018.05.001`` ``foss/2018b``, ``intel/2018b`` ``2018.11.001`` ``intel/2019a`` +``2019.11.001`` ``foss/2019b``, ``intel/2019b`` =================== ================================================ @@ -6667,6 +7074,23 @@ version toolchain ========= ============== +.. _list_software_ELSI_301: + +*ELSI* +++++++ + +ELSI provides and enhances scalable, open-source software library solutions for electronic structure calculations in materials science, condensed matter physics, chemistry, and many other fields. ELSI focuses on methods that solve or circumvent eigenvalue problems in electronic structure theory. The ELSI infrastructure should also be useful for other challenging eigenvalue problems. + +*homepage*: https://wordpress.elsi-interchange.org/ + +========= ============= =============== +version versionsuffix toolchain +========= ============= =============== +``2.5.0`` ``intel/2019b`` +``2.5.0`` ``-PEXSI`` ``intel/2019b`` +========= ============= =============== + + .. _list_software_Emacs_489: *Emacs* @@ -6719,6 +7143,7 @@ EMBOSS is 'The European Molecular Biology Open Software Suite'. EMBOSS is a fre version versionsuffix toolchain ========= ================= ================================================================================================================================ ``6.6.0`` ``GCC/8.2.0-2.31.1``, ``foss/2016b``, ``foss/2018b``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``intel/2017a``, ``intel/2018b`` +``6.6.0`` ``-Java-11`` ``GCC/8.3.0`` ``6.6.0`` ``-X11-20170314`` ``intel/2017a`` ========= ================= ================================================================================================================================ @@ -6773,6 +7198,22 @@ version toolchain ========= =============== +.. _list_software_EnsEMBLCoreAPI_1193: + +*EnsEMBLCoreAPI* +++++++++++++++++ + +The Ensembl Core Perl API and SQL schema + +*homepage*: https://www.ensembl.org/info/docs/api/index.html + +================== ================ ============== +version versionsuffix toolchain +================== ================ ============== +``96.0-r20190601`` ``-Perl-5.28.1`` ``foss/2019a`` +================== ================ ============== + + .. _list_software_entrypoints_1231: *entrypoints* @@ -7068,7 +7509,7 @@ version toolchain --- -:ref:`list_software_f90cache_707` - :ref:`list_software_Faber_480` - :ref:`list_software_faceswap_842` - :ref:`list_software_FALCON_435` - :ref:`list_software_FANN_291` - :ref:`list_software_fast5_483` - :ref:`list_software_FASTA_367` - :ref:`list_software_FastaIndex_999` - :ref:`list_software_FastANI_614` - :ref:`list_software_FastME_544` - :ref:`list_software_fastp_542` - :ref:`list_software_fastPHASE_799` - :ref:`list_software_fastq-tools_1149` - :ref:`list_software_FastQ_Screen_1182` - :ref:`list_software_FastQC_546` - :ref:`list_software_FastQTL_639` - :ref:`list_software_fastqz_665` - :ref:`list_software_FastRFS_633` - :ref:`list_software_fastStructure_1407` - :ref:`list_software_FastTree_798` - :ref:`list_software_FASTX-Toolkit_1177` - :ref:`list_software_fatslim_752` - :ref:`list_software_fbm_309` - :ref:`list_software_FCM_214` - :ref:`list_software_FDS_221` - :ref:`list_software_fdstools_878` - :ref:`list_software_FDTD_Solutions_1361` - :ref:`list_software_feh_307` - :ref:`list_software_Ferret_616` - :ref:`list_software_FFC_207` - :ref:`list_software_FFLAS-FFPACK_836` - :ref:`list_software_FFmpeg_565` - :ref:`list_software_ffnet_531` - :ref:`list_software_FFTW_311` - :ref:`list_software_FGSL_300` - :ref:`list_software_FIAT_292` - :ref:`list_software_Fiji_386` - :ref:`list_software_file_416` - :ref:`list_software_Filtlong_831` - :ref:`list_software_find_circ_929` - :ref:`list_software_findhap_730` - :ref:`list_software_findutils_978` - :ref:`list_software_fineRADstructure_1642` - :ref:`list_software_fineSTRUCTURE_1139` - :ref:`list_software_Firefox_723` - :ref:`list_software_FireWorks_924` - :ref:`list_software_fixesproto_1107` - :ref:`list_software_FLANN_367` - :ref:`list_software_FLASH_366` - :ref:`list_software_Flask_497` - :ref:`list_software_FLEUR_382` - :ref:`list_software_flex_431` - :ref:`list_software_FlexiDot_799` - :ref:`list_software_FLINT_381` - :ref:`list_software_FLTK_305` - :ref:`list_software_FLUENT_462` - :ref:`list_software_Flye_400` - :ref:`list_software_FMILibrary_945` - :ref:`list_software_FMRIprep_741` - :ref:`list_software_fmt_327` - :ref:`list_software_FoldX_477` - :ref:`list_software_fontconfig_1069` - :ref:`list_software_fontsproto_1118` - :ref:`list_software_foss_443` - :ref:`list_software_fosscuda_856` - :ref:`list_software_FoX_269` - :ref:`list_software_FPM_227` - :ref:`list_software_fqtrim_659` - :ref:`list_software_fqzcomp_768` - :ref:`list_software_FragGeneScan_1156` - :ref:`list_software_FRANz_417` - :ref:`list_software_FreeFem++_752` - :ref:`list_software_freeglut_862` - :ref:`list_software_FreeImage_869` - :ref:`list_software_FreeSurfer_1017` - :ref:`list_software_freetype_868` - :ref:`list_software_FreeXL_550` - :ref:`list_software_FriBidi_665` - :ref:`list_software_FSL_229` - :ref:`list_software_FSLeyes_667` - :ref:`list_software_FTGL_301` - :ref:`list_software_fullrmc_757` - :ref:`list_software_FUNWAVE-TVD_823` - :ref:`list_software_FUSE_307` - :ref:`list_software_future_667` - :ref:`list_software_fxtract_764` +:ref:`list_software_f90cache_707` - :ref:`list_software_Faber_480` - :ref:`list_software_faceswap_842` - :ref:`list_software_FALCON_435` - :ref:`list_software_FANN_291` - :ref:`list_software_fast5_483` - :ref:`list_software_FASTA_367` - :ref:`list_software_FastaIndex_999` - :ref:`list_software_FastANI_614` - :ref:`list_software_FastME_544` - :ref:`list_software_fastp_542` - :ref:`list_software_fastPHASE_799` - :ref:`list_software_fastq-pair_1016` - :ref:`list_software_fastq-tools_1149` - :ref:`list_software_FastQ_Screen_1182` - :ref:`list_software_FastQC_546` - :ref:`list_software_FastQTL_639` - :ref:`list_software_fastqz_665` - :ref:`list_software_FastRFS_633` - :ref:`list_software_fastStructure_1407` - :ref:`list_software_FastTree_798` - :ref:`list_software_FASTX-Toolkit_1177` - :ref:`list_software_fatslim_752` - :ref:`list_software_fbm_309` - :ref:`list_software_FCM_214` - :ref:`list_software_FDS_221` - :ref:`list_software_fdstools_878` - :ref:`list_software_FDTD_Solutions_1361` - :ref:`list_software_feh_307` - :ref:`list_software_Ferret_616` - :ref:`list_software_FFC_207` - :ref:`list_software_FFLAS-FFPACK_836` - :ref:`list_software_FFmpeg_565` - :ref:`list_software_ffnet_531` - :ref:`list_software_FFTW_311` - :ref:`list_software_FGSL_300` - :ref:`list_software_FIAT_292` - :ref:`list_software_FigureGen_892` - :ref:`list_software_Fiji_386` - :ref:`list_software_file_416` - :ref:`list_software_Filtlong_831` - :ref:`list_software_find_circ_929` - :ref:`list_software_findhap_730` - :ref:`list_software_findutils_978` - :ref:`list_software_fineRADstructure_1642` - :ref:`list_software_fineSTRUCTURE_1139` - :ref:`list_software_Fiona_493` - :ref:`list_software_Firefox_723` - :ref:`list_software_FireWorks_924` - :ref:`list_software_fixesproto_1107` - :ref:`list_software_FLANN_367` - :ref:`list_software_FLASH_366` - :ref:`list_software_Flask_497` - :ref:`list_software_FLEUR_382` - :ref:`list_software_flex_431` - :ref:`list_software_FlexiDot_799` - :ref:`list_software_FLINT_381` - :ref:`list_software_FLTK_305` - :ref:`list_software_FLUENT_462` - :ref:`list_software_Flye_400` - :ref:`list_software_FMILibrary_945` - :ref:`list_software_FMRIprep_741` - :ref:`list_software_fmt_327` - :ref:`list_software_FoldX_477` - :ref:`list_software_fontconfig_1069` - :ref:`list_software_fontsproto_1118` - :ref:`list_software_foss_443` - :ref:`list_software_fosscuda_856` - :ref:`list_software_FoX_269` - :ref:`list_software_FPM_227` - :ref:`list_software_fqtrim_659` - :ref:`list_software_fqzcomp_768` - :ref:`list_software_FragGeneScan_1156` - :ref:`list_software_FRANz_417` - :ref:`list_software_FreeFem++_752` - :ref:`list_software_freeglut_862` - :ref:`list_software_FreeImage_869` - :ref:`list_software_FreeSurfer_1017` - :ref:`list_software_freetype_868` - :ref:`list_software_FreeXL_550` - :ref:`list_software_FriBidi_665` - :ref:`list_software_FSL_229` - :ref:`list_software_FSLeyes_667` - :ref:`list_software_FTGL_301` - :ref:`list_software_fullrmc_757` - :ref:`list_software_FUNWAVE-TVD_823` - :ref:`list_software_FUSE_307` - :ref:`list_software_FuSeq_484` - :ref:`list_software_future_667` - :ref:`list_software_fxtract_764` .. _list_software_f90cache_707: @@ -7128,11 +7569,12 @@ Falcon: a set of tools for fast aligning long reads for consensus and assembly *homepage*: https://github.com/PacificBiosciences/FALCON -========= =============== -version toolchain -========= =============== -``1.8.8`` ``intel/2017b`` -========= =============== +========= ================== =============== +version versionsuffix toolchain +========= ================== =============== +``1.8.8`` ``intel/2017b`` +``1.8.8`` ``-Python-2.7.16`` ``intel/2019b`` +========= ================== =============== .. _list_software_FANN_291: @@ -7213,6 +7655,7 @@ version toolchain ======= ============================================================== ``1.1`` ``foss/2018b``, ``intel/2018b`` ``1.2`` ``GCC/8.2.0-2.31.1``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1`` +``1.3`` ``iccifort/2019.5.281`` ======= ============================================================== @@ -7225,12 +7668,12 @@ FastME: a comprehensive, accurate and fast distance-based phylogeny inference pr *homepage*: http://www.atgc-montpellier.fr/fastme/ -=========== ================================ -version toolchain -=========== ================================ -``2.1.5`` ``foss/2016a`` -``2.1.6.1`` ``intel/2018a``, ``intel/2018b`` -=========== ================================ +=========== ======================================================================== +version toolchain +=========== ======================================================================== +``2.1.5`` ``foss/2016a`` +``2.1.6.1`` ``GCC/8.3.0``, ``iccifort/2019.5.281``, ``intel/2018a``, ``intel/2018b`` +=========== ======================================================================== .. _list_software_fastp_542: @@ -7242,12 +7685,12 @@ A tool designed to provide fast all-in-one preprocessing for FastQ files. This *homepage*: https://github.com/OpenGene/fastp -========== ============================================= -version toolchain -========== ============================================= -``0.19.7`` ``foss/2018b`` -``0.20.0`` ``GCC/8.2.0-2.31.1``, ``iccifort/2019.5.281`` -========== ============================================= +========== ============================================================ +version toolchain +========== ============================================================ +``0.19.7`` ``foss/2018b`` +``0.20.0`` ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0``, ``iccifort/2019.5.281`` +========== ============================================================ .. _list_software_fastPHASE_799: @@ -7266,6 +7709,22 @@ version toolchain ========= ========== +.. _list_software_fastq-pair_1016: + +*fastq-pair* +++++++++++++ + +Match up paired end fastq files quickly and efficiently. + +*homepage*: https://github.com/linsalrob/fastq-pair + +======= ================= +version toolchain +======= ================= +``1.0`` ``GCCcore/8.2.0`` +======= ================= + + .. _list_software_fastq-tools_1149: *fastq-tools* @@ -7324,6 +7783,7 @@ version versionsuffix toolchain ``0.11.7`` ``-Java-1.8.0_162`` ``system`` ``0.11.8`` ``-Java-1.8`` ``system`` ``0.11.8`` ``-Java-11`` ``system`` +``0.11.9`` ``-Java-11`` ``system`` ========== =================== ========== @@ -7407,7 +7867,7 @@ FastTree infers approximately-maximum-likelihood phylogenetic trees from alignme version toolchain ========== ================================================================= ``2.1.10`` ``foss/2018b``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b`` -``2.1.11`` ``GCCcore/8.2.0`` +``2.1.11`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` ========== ================================================================= @@ -7553,13 +8013,14 @@ version toolchain Ferret is an interactive computer visualization and analysis environment designed to meet the needs of oceanographers and meteorologists analyzing large and complex gridded data sets. -*homepage*: http://ferret.pmel.noaa.gov/ +*homepage*: https://ferret.pmel.noaa.gov/Ferret/ -======= =============== -version toolchain -======= =============== -``7.3`` ``intel/2017b`` -======= =============== +========= =============== +version toolchain +========= =============== +``7.3`` ``intel/2017b`` +``7.5.0`` ``foss/2019b`` +========= =============== .. _list_software_FFC_207: @@ -7697,6 +8158,22 @@ version versionsuffix toolchain ============ ================== =============================== +.. _list_software_FigureGen_892: + +*FigureGen* ++++++++++++ + +FigureGen is a Fortran program that creates images for ADCIRC files. It reads mesh files (fort.14, etc.), nodal attributes files (fort.13, etc.) and output files (fort.63, fort.64, maxele.63, etc.). It plots contours, contour lines, and vectors. Using FigureGen, you can go directly from the ADCIRC input and output files to a presentation-quality figure, for one or multiple time snaps. + +*homepage*: https://ccht.ccee.ncsu.edu/category/software/figuregen/ + +=============== ============== +version toolchain +=============== ============== +``51-20190516`` ``foss/2019a`` +=============== ============== + + .. _list_software_Fiji_386: *Fiji* @@ -7831,6 +8308,22 @@ version toolchain ========= =============== +.. _list_software_Fiona_493: + +*Fiona* ++++++++ + +Fiona is designed to be simple and dependable. It focuses on reading and writing data in standard Python IO style and relies upon familiar Python types and protocols such as files, dictionaries, mappings, and iterators instead of classes specific to OGR. Fiona can read and write real-world data using multi-layered GIS formats and zipped virtual file systems and integrates readily with other Python GIS packages such as pyproj, Rtree, and Shapely. + +*homepage*: https://github.com/Toblerity/Fiona + +========== ================= ============== +version versionsuffix toolchain +========== ================= ============== +``1.8.13`` ``-Python-3.7.4`` ``foss/2019b`` +========== ================= ============== + + .. _list_software_Firefox_723: *Firefox* @@ -7954,17 +8447,17 @@ Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, some *homepage*: http://flex.sourceforge.net/ -========== ================================================================================================================================================================================================================================================================================================================================================= -version toolchain -========== ================================================================================================================================================================================================================================================================================================================================================= -``2.5.35`` ``system`` -``2.5.38`` ``GCC/4.8.2`` -``2.5.39`` ``GCC/4.9.2``, ``GCC/4.9.2-binutils-2.25``, ``GCC/4.9.3``, ``GCC/4.9.3-binutils-2.25``, ``GCC/5.1.0-binutils-2.25``, ``GCCcore/4.9.2``, ``GCCcore/4.9.3``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/8.2.0``, ``GNU/4.9.3-2.25``, ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016.02-GCC-4.9``, ``intel/2016a``, ``intel/2016b``, ``system`` -``2.6.0`` ``GCC/4.9.2``, ``GCCcore/4.9.3``, ``GCCcore/4.9.4``, ``GCCcore/5.3.0``, ``GCCcore/5.4.0``, ``GCCcore/6.1.0``, ``GCCcore/6.2.0``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``intel/2016a``, ``intel/2016b``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25``, ``system`` -``2.6.2`` ``intel/2016b`` -``2.6.3`` ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``GCCcore/7.1.0``, ``gimkl/2017a``, ``system`` -``2.6.4`` ``GCCcore/5.5.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/7.4.0``, ``GCCcore/8.1.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.1.0``, ``GCCcore/9.2.0``, ``GCCcore/system``, ``system`` -========== ================================================================================================================================================================================================================================================================================================================================================= +========== ==================================================================================================================================================================================================================================================================================================================================================================== +version toolchain +========== ==================================================================================================================================================================================================================================================================================================================================================================== +``2.5.35`` ``system`` +``2.5.38`` ``GCC/4.8.2`` +``2.5.39`` ``GCC/4.9.2``, ``GCC/4.9.2-binutils-2.25``, ``GCC/4.9.3``, ``GCC/4.9.3-binutils-2.25``, ``GCC/5.1.0-binutils-2.25``, ``GCCcore/4.9.2``, ``GCCcore/4.9.3``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GNU/4.9.3-2.25``, ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016.02-GCC-4.9``, ``intel/2016a``, ``intel/2016b``, ``system`` +``2.6.0`` ``GCC/4.9.2``, ``GCCcore/4.9.3``, ``GCCcore/4.9.4``, ``GCCcore/5.3.0``, ``GCCcore/5.4.0``, ``GCCcore/6.1.0``, ``GCCcore/6.2.0``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``intel/2016a``, ``intel/2016b``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25``, ``system`` +``2.6.2`` ``intel/2016b`` +``2.6.3`` ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``GCCcore/7.1.0``, ``gimkl/2017a``, ``system`` +``2.6.4`` ``GCCcore/5.5.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/7.4.0``, ``GCCcore/8.1.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.1.0``, ``GCCcore/9.2.0``, ``GCCcore/9.3.0``, ``GCCcore/system``, ``system`` +========== ==================================================================================================================================================================================================================================================================================================================================================================== .. _list_software_FlexiDot_799: @@ -8052,6 +8545,7 @@ version versionsuffix toolchain ======= ================== =============== ``2.4`` ``-Python-2.7.15`` ``intel/2018b`` ``2.6`` ``-Python-3.7.2`` ``foss/2019a`` +``2.6`` ``-Python-3.7.4`` ``intel/2019b`` ======= ================== =============== @@ -8353,11 +8847,11 @@ FreeImage is an Open Source library project for developers who would like to sup *homepage*: http://freeimage.sourceforge.net -========== ================= -version toolchain -========== ================= -``3.18.0`` ``GCCcore/7.3.0`` -========== ================= +========== ==================================== +version toolchain +========== ==================================== +``3.18.0`` ``GCCcore/7.3.0``, ``GCCcore/8.3.0`` +========== ==================================== .. _list_software_FreeSurfer_1017: @@ -8549,6 +9043,22 @@ version toolchain ========= =============== +.. _list_software_FuSeq_484: + +*FuSeq* ++++++++ + +FuSeq is a novel method to discover fusion genes from paired-end RNA sequencing data. + +*homepage*: https://github.com/nghiavtr/FuSeq + +========= =============== +version toolchain +========= =============== +``1.1.2`` ``gompi/2019b`` +========= =============== + + .. _list_software_future_667: *future* @@ -8590,7 +9100,7 @@ version toolchain --- -:ref:`list_software_g2clib_563` - :ref:`list_software_g2lib_464` - :ref:`list_software_g2log_475` - :ref:`list_software_Gaia_370` - :ref:`list_software_GAMESS-US_661` - :ref:`list_software_gap_312` - :ref:`list_software_GapCloser_896` - :ref:`list_software_GapFiller_886` - :ref:`list_software_GARLI_367` - :ref:`list_software_GAT_220` - :ref:`list_software_GATE_289` - :ref:`list_software_GATK_295` - :ref:`list_software_Gblocks_709` - :ref:`list_software_gbs2ploidy_1023` - :ref:`list_software_gc_202` - :ref:`list_software_GC3Pie_475` - :ref:`list_software_GCC_205` - :ref:`list_software_GCCcore_630` - :ref:`list_software_gcccuda_714` - :ref:`list_software_GConf_461` - :ref:`list_software_Gctf_388` - :ref:`list_software_GD_139` - :ref:`list_software_GDAL_280` - :ref:`list_software_GDB_205` - :ref:`list_software_gdbgui_626` - :ref:`list_software_gdc-client_986` - :ref:`list_software_GDCHART_509` - :ref:`list_software_GDCM_283` - :ref:`list_software_GDGraph_637` - :ref:`list_software_gdist_539` - :ref:`list_software_Gdk-Pixbuf_945` - :ref:`list_software_Geant4_547` - :ref:`list_software_gearshifft_1059` - :ref:`list_software_GEM-library_1019` - :ref:`list_software_GEMMA_359` - :ref:`list_software_gencore_variant_detection_2645` - :ref:`list_software_GeneMark-ET_976` - :ref:`list_software_GenomeMapper_1216` - :ref:`list_software_GenomeTester4_1286` - :ref:`list_software_GenomeThreader_1418` - :ref:`list_software_GenotypeHarmonizer_1898` - :ref:`list_software_gensim_643` - :ref:`list_software_geopy_548` - :ref:`list_software_GEOS_302` - :ref:`list_software_Gerris_620` - :ref:`list_software_GETORB_451` - :ref:`list_software_gettext_773` - :ref:`list_software_GffCompare_986` - :ref:`list_software_gffread_719` - :ref:`list_software_gflags_628` - :ref:`list_software_GFOLD_364` - :ref:`list_software_GHC_210` - :ref:`list_software_Ghostscript_1178` - :ref:`list_software_giflib_621` - :ref:`list_software_gifsicle_838` - :ref:`list_software_GIMIC_361` - :ref:`list_software_gimkl_532` - :ref:`list_software_gimpi_534` - :ref:`list_software_gimpic_633` - :ref:`list_software_GIMPS_384` - :ref:`list_software_giolf_529` - :ref:`list_software_giolfc_628` - :ref:`list_software_git_324` - :ref:`list_software_git-lfs_694` - :ref:`list_software_GitPython_934` - :ref:`list_software_Givaro_616` - :ref:`list_software_Giza_395` - :ref:`list_software_GL2PS_360` - :ref:`list_software_Glade_477` - :ref:`list_software_glew_431` - :ref:`list_software_GLib_350` - :ref:`list_software_glibc_513` - :ref:`list_software_GLibmm_568` - :ref:`list_software_GLIMMER_525` - :ref:`list_software_GlimmerHMM_943` - :ref:`list_software_GLM_224` - :ref:`list_software_GlobalArrays_1219` - :ref:`list_software_Globus-CLI_881` - :ref:`list_software_GlobusConnectPersonal_2170` - :ref:`list_software_glog_425` - :ref:`list_software_GLPK_302` - :ref:`list_software_glproto_775` - :ref:`list_software_GMAP-GSNAP_715` - :ref:`list_software_GMP_228` - :ref:`list_software_gmpich_632` - :ref:`list_software_gmpolf_645` - :ref:`list_software_gmpy2_495` - :ref:`list_software_gmsh_431` - :ref:`list_software_GMT_232` - :ref:`list_software_gmvapich2_897` - :ref:`list_software_gmvolf_651` - :ref:`list_software_GNU_234` - :ref:`list_software_gnuplot_777` - :ref:`list_software_GnuTLS_541` - :ref:`list_software_Go_182` - :ref:`list_software_GObject-Introspection_2108` - :ref:`list_software_golf_424` - :ref:`list_software_gomkl_538` - :ref:`list_software_gompi_540` - :ref:`list_software_gompic_639` - :ref:`list_software_google-java-format_1794` - :ref:`list_software_googletest_1085` - :ref:`list_software_GP2C_268` - :ref:`list_software_GPAW_303` - :ref:`list_software_GPAW-setups_1024` - :ref:`list_software_gperf_532` - :ref:`list_software_gperftools_1093` - :ref:`list_software_gpustat_776` - :ref:`list_software_Grace_482` - :ref:`list_software_grace_514` - :ref:`list_software_Gradle_591` - :ref:`list_software_gradunwarp_1083` - :ref:`list_software_graph-tool_1021` - :ref:`list_software_Graphene_810` - :ref:`list_software_GraphicsMagick_1405` - :ref:`list_software_Graphviz_843` - :ref:`list_software_graphviz_875` - :ref:`list_software_GRASS_384` - :ref:`list_software_Greenlet_822` - :ref:`list_software_Grep_398` - :ref:`list_software_grib_api_829` - :ref:`list_software_GRIT_310` - :ref:`list_software_GRNBoost_750` - :ref:`list_software_GroIMP_526` - :ref:`list_software_GROMACS_524` - :ref:`list_software_GromacsWrapper_1453` - :ref:`list_software_GroopM_596` - :ref:`list_software_gsettings-desktop-schemas_2576` - :ref:`list_software_GSL_230` - :ref:`list_software_gSOAP_410` - :ref:`list_software_GST-plugins-base_1509` - :ref:`list_software_GStreamer_906` - :ref:`list_software_GTDB-Tk_525` - :ref:`list_software_gtest_551` - :ref:`list_software_GTK+_273` - :ref:`list_software_GtkSourceView_1330` - :ref:`list_software_GTOOL_389` - :ref:`list_software_GTS_238` - :ref:`list_software_guenomu_768` - :ref:`list_software_Guile_502` - :ref:`list_software_GULP_312` - :ref:`list_software_Gurobi_616` - :ref:`list_software_gzip_442` +:ref:`list_software_g2clib_563` - :ref:`list_software_g2lib_464` - :ref:`list_software_g2log_475` - :ref:`list_software_Gaia_370` - :ref:`list_software_GAMESS-US_661` - :ref:`list_software_gap_312` - :ref:`list_software_GapCloser_896` - :ref:`list_software_GapFiller_886` - :ref:`list_software_GARLI_367` - :ref:`list_software_GAT_220` - :ref:`list_software_GATE_289` - :ref:`list_software_GATK_295` - :ref:`list_software_Gblocks_709` - :ref:`list_software_gbs2ploidy_1023` - :ref:`list_software_gc_202` - :ref:`list_software_GC3Pie_475` - :ref:`list_software_GCC_205` - :ref:`list_software_GCCcore_630` - :ref:`list_software_gcccuda_714` - :ref:`list_software_GConf_461` - :ref:`list_software_Gctf_388` - :ref:`list_software_GD_139` - :ref:`list_software_GDAL_280` - :ref:`list_software_GDB_205` - :ref:`list_software_gdbgui_626` - :ref:`list_software_gdc-client_986` - :ref:`list_software_GDCHART_509` - :ref:`list_software_GDCM_283` - :ref:`list_software_GDGraph_637` - :ref:`list_software_gdist_539` - :ref:`list_software_Gdk-Pixbuf_945` - :ref:`list_software_Geant4_547` - :ref:`list_software_gearshifft_1059` - :ref:`list_software_GEM-library_1019` - :ref:`list_software_GEMMA_359` - :ref:`list_software_gencore_variant_detection_2645` - :ref:`list_software_GeneMark-ET_976` - :ref:`list_software_GenomeMapper_1216` - :ref:`list_software_GenomeTester4_1286` - :ref:`list_software_GenomeThreader_1418` - :ref:`list_software_GenomeTools_1132` - :ref:`list_software_GenotypeHarmonizer_1898` - :ref:`list_software_gensim_643` - :ref:`list_software_geopy_548` - :ref:`list_software_GEOS_302` - :ref:`list_software_Gerris_620` - :ref:`list_software_GETORB_451` - :ref:`list_software_gettext_773` - :ref:`list_software_GffCompare_986` - :ref:`list_software_gffread_719` - :ref:`list_software_gflags_628` - :ref:`list_software_GFOLD_364` - :ref:`list_software_GHC_210` - :ref:`list_software_Ghostscript_1178` - :ref:`list_software_giflib_621` - :ref:`list_software_gifsicle_838` - :ref:`list_software_GIMIC_361` - :ref:`list_software_gimkl_532` - :ref:`list_software_gimpi_534` - :ref:`list_software_gimpic_633` - :ref:`list_software_GIMPS_384` - :ref:`list_software_giolf_529` - :ref:`list_software_giolfc_628` - :ref:`list_software_git_324` - :ref:`list_software_git-lfs_694` - :ref:`list_software_GitPython_934` - :ref:`list_software_Givaro_616` - :ref:`list_software_Giza_395` - :ref:`list_software_GL2PS_360` - :ref:`list_software_Glade_477` - :ref:`list_software_glew_431` - :ref:`list_software_GLib_350` - :ref:`list_software_glibc_513` - :ref:`list_software_GLibmm_568` - :ref:`list_software_GLIMMER_525` - :ref:`list_software_GlimmerHMM_943` - :ref:`list_software_GLM_224` - :ref:`list_software_GlobalArrays_1219` - :ref:`list_software_Globus-CLI_881` - :ref:`list_software_GlobusConnectPersonal_2170` - :ref:`list_software_glog_425` - :ref:`list_software_GLPK_302` - :ref:`list_software_glproto_775` - :ref:`list_software_GMAP-GSNAP_715` - :ref:`list_software_GMP_228` - :ref:`list_software_gmpich_632` - :ref:`list_software_gmpolf_645` - :ref:`list_software_gmpy2_495` - :ref:`list_software_gmsh_431` - :ref:`list_software_GMT_232` - :ref:`list_software_gmvapich2_897` - :ref:`list_software_gmvolf_651` - :ref:`list_software_GNU_234` - :ref:`list_software_gnuplot_777` - :ref:`list_software_GnuTLS_541` - :ref:`list_software_Go_182` - :ref:`list_software_GObject-Introspection_2108` - :ref:`list_software_golf_424` - :ref:`list_software_gomkl_538` - :ref:`list_software_gompi_540` - :ref:`list_software_gompic_639` - :ref:`list_software_google-java-format_1794` - :ref:`list_software_googletest_1085` - :ref:`list_software_GP2C_268` - :ref:`list_software_GPAW_303` - :ref:`list_software_GPAW-setups_1024` - :ref:`list_software_gperf_532` - :ref:`list_software_gperftools_1093` - :ref:`list_software_gpustat_776` - :ref:`list_software_Grace_482` - :ref:`list_software_grace_514` - :ref:`list_software_Gradle_591` - :ref:`list_software_gradunwarp_1083` - :ref:`list_software_graph-tool_1021` - :ref:`list_software_Graphene_810` - :ref:`list_software_GraphicsMagick_1405` - :ref:`list_software_GraphMap2_834` - :ref:`list_software_Graphviz_843` - :ref:`list_software_graphviz_875` - :ref:`list_software_GRASP_381` - :ref:`list_software_GRASS_384` - :ref:`list_software_Greenlet_822` - :ref:`list_software_Grep_398` - :ref:`list_software_grib_api_829` - :ref:`list_software_GRIT_310` - :ref:`list_software_GRNBoost_750` - :ref:`list_software_GroIMP_526` - :ref:`list_software_GROMACS_524` - :ref:`list_software_GromacsWrapper_1453` - :ref:`list_software_GroopM_596` - :ref:`list_software_Groovy_646` - :ref:`list_software_gsettings-desktop-schemas_2576` - :ref:`list_software_GSL_230` - :ref:`list_software_gSOAP_410` - :ref:`list_software_gsport_671` - :ref:`list_software_GST-plugins-base_1509` - :ref:`list_software_GStreamer_906` - :ref:`list_software_GTDB-Tk_525` - :ref:`list_software_gtest_551` - :ref:`list_software_GTK+_273` - :ref:`list_software_GtkSourceView_1330` - :ref:`list_software_GTOOL_389` - :ref:`list_software_GTS_238` - :ref:`list_software_gubbins_746` - :ref:`list_software_guenomu_768` - :ref:`list_software_Guile_502` - :ref:`list_software_GULP_312` - :ref:`list_software_Gurobi_616` - :ref:`list_software_gzip_442` .. _list_software_g2clib_563: @@ -8635,11 +9145,11 @@ g2log, efficient asynchronous logger using C++11 *homepage*: https://sites.google.com/site/kjellhedstrom2//g2log-efficient-background-io-processign-with-c11 -======= ============== -version toolchain -======= ============== -``1.0`` ``foss/2016b`` -======= ============== +======= ================================= +version toolchain +======= ================================= +``1.0`` ``GCCcore/8.3.0``, ``foss/2016b`` +======= ================================= .. _list_software_Gaia_370: @@ -8821,6 +9331,7 @@ version versionsuffix toolchain ``4.1.0.0`` ``-Python-3.6.6`` ``foss/2018b`` ``4.1.2.0`` ``-Java-1.8`` ``GCCcore/8.2.0`` ``4.1.3.0`` ``-Java-1.8`` ``GCCcore/8.3.0`` +``4.1.4.1`` ``-Java-11`` ``GCCcore/8.3.0`` ============ =================== ================= @@ -8953,6 +9464,7 @@ version versionsuffix toolchain ``8.3.0`` ``system`` ``8.3.0`` ``-2.32`` ``system`` ``9.1.0`` ``-2.32`` ``system`` +``9.2.0`` ``system`` ``9.2.0`` ``-2.32`` ``system`` ``system`` ``system`` ``system`` ``-2.29`` ``system`` @@ -8991,6 +9503,7 @@ version toolchain ``8.3.0`` ``system`` ``9.1.0`` ``system`` ``9.2.0`` ``system`` +``9.3.0`` ``system`` ``system`` ``system`` ========== ========== @@ -9098,7 +9611,7 @@ version versionsuffix toolchain ``2.2.3`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` ``3.0.0`` ``-Python-2.7.15`` ``foss/2019a``, ``intel/2019a`` ``3.0.0`` ``-Python-3.7.2`` ``foss/2019a``, ``intel/2019a`` -``3.0.2`` ``-Python-3.7.4`` ``intel/2019b`` +``3.0.2`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` ========= ============================== ================================================================ @@ -9109,7 +9622,7 @@ version versionsuffix toolchain The GNU Project Debugger -*homepage*: http://www.gnu.org/software/gdb/gdb.html +*homepage*: https://www.gnu.org/software/gdb/gdb.html ========== ================== =============================== version versionsuffix toolchain @@ -9124,6 +9637,7 @@ version versionsuffix toolchain ``8.1`` ``-Python-2.7.14`` ``foss/2018a`` ``8.1.1`` ``-Python-2.7.14`` ``intel/2018a`` ``8.3`` ``-Python-3.7.2`` ``GCCcore/8.2.0`` +``9.1`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` ========== ================== =============================== @@ -9248,6 +9762,7 @@ version toolchain ``2.36.11`` ``foss/2017b``, ``foss/2018a``, ``fosscuda/2018b``, ``intel/2017b``, ``intel/2018a`` ``2.36.12`` ``foss/2018b``, ``fosscuda/2018b`` ``2.38.1`` ``GCCcore/8.2.0`` +``2.38.2`` ``GCCcore/8.3.0`` =========== ==================================================================================== @@ -9402,6 +9917,25 @@ version versionsuffix toolchain ========= ======================= ========== +.. _list_software_GenomeTools_1132: + +*GenomeTools* ++++++++++++++ + +A comprehensive software library for efficient processing of structured genome annotations. + +*homepage*: http://genometools.org + +========== ================== ============== +version versionsuffix toolchain +========== ================== ============== +``1.5.10`` ``foss/2018b`` +``1.5.10`` ``-Python-2.7.15`` ``foss/2018b`` +``1.6.1`` ``GCC/8.3.0`` +``1.6.1`` ``-Python-2.7.16`` ``GCC/8.3.0`` +========== ================== ============== + + .. _list_software_GenotypeHarmonizer_1898: *GenotypeHarmonizer* @@ -9475,7 +10009,7 @@ version versionsuffix toolchain ``3.6.2`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` ``3.7.2`` ``-Python-2.7.15`` ``foss/2019a``, ``intel/2019a`` ``3.7.2`` ``-Python-3.7.2`` ``foss/2019a``, ``intel/2019a`` -``3.8.0`` ``-Python-3.7.4`` ``iccifort/2019.5.281`` +``3.8.0`` ``-Python-3.7.4`` ``GCC/8.3.0``, ``iccifort/2019.5.281`` ========= ================== ================================================================ @@ -9899,13 +10433,13 @@ GL2PS: an OpenGL to PostScript printing library *homepage*: http://www.geuz.org/gl2ps/ -========= ================ ================================================================================================= -version versionsuffix toolchain -========= ================ ================================================================================================= -``1.3.9`` ``foss/2016a``, ``foss/2016b``, ``intel/2016a``, ``intel/2016b`` -``1.3.9`` ``-Mesa-11.2.1`` ``foss/2016a``, ``intel/2016a`` -``1.4.0`` ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``intel/2017a``, ``intel/2017b``, ``intel/2018a`` -========= ================ ================================================================================================= +========= ================ ==================================================================================================================================== +version versionsuffix toolchain +========= ================ ==================================================================================================================================== +``1.3.9`` ``foss/2016a``, ``foss/2016b``, ``intel/2016a``, ``intel/2016b`` +``1.3.9`` ``-Mesa-11.2.1`` ``foss/2016a``, ``intel/2016a`` +``1.4.0`` ``GCCcore/8.3.0``, ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``foss/2019a``, ``intel/2017a``, ``intel/2017b``, ``intel/2018a`` +========= ================ ==================================================================================================================================== .. _list_software_Glade_477: @@ -10129,14 +10663,14 @@ The GLPK (GNU Linear Programming Kit) package is intended for solving large-sca *homepage*: https://www.gnu.org/software/glpk/ -======== ======================================================= -version toolchain -======== ======================================================= -``4.58`` ``foss/2016a``, ``intel/2016a`` -``4.60`` ``GCCcore/5.4.0``, ``intel/2016b`` -``4.61`` ``intel/2017a`` -``4.65`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` -======== ======================================================= +======== ========================================================================== +version toolchain +======== ========================================================================== +``4.58`` ``foss/2016a``, ``intel/2016a`` +``4.60`` ``GCCcore/5.4.0``, ``intel/2016b`` +``4.61`` ``intel/2017a`` +``4.65`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` +======== ========================================================================== .. _list_software_glproto_775: @@ -10172,6 +10706,7 @@ version toolchain ``2018-05-11`` ``intel/2018a`` ``2018-07-04`` ``intel/2018a`` ``2019-03-15`` ``foss/2018b`` +``2019-09-12`` ``GCC/8.3.0`` ============== =============== @@ -10347,7 +10882,7 @@ version toolchain Portable interactive, function plotting utility -*homepage*: http://gnuplot.sourceforge.net/ +*homepage*: https://gnuplot.sourceforge.net/ ========= ================================================================ version toolchain @@ -10358,6 +10893,7 @@ version toolchain ``5.2.2`` ``foss/2017b``, ``foss/2018a``, ``intel/2017b``, ``intel/2018a`` ``5.2.5`` ``foss/2018b`` ``5.2.6`` ``GCCcore/8.2.0``, ``foss/2018b``, ``fosscuda/2018b`` +``5.2.8`` ``GCCcore/8.3.0`` ========= ================================================================ @@ -10399,6 +10935,8 @@ version toolchain ``1.12`` ``system`` ``1.12.1`` ``GCCcore/7.3.0`` ``1.13.1`` ``system`` +``1.14`` ``system`` +``1.14.1`` ``system`` ========== ================= @@ -10424,7 +10962,9 @@ version versionsuffix toolchain ``1.54.1`` ``-Python-2.7.14`` ``foss/2018a``, ``intel/2018a`` ``1.54.1`` ``-Python-2.7.15`` ``foss/2018b``, ``fosscuda/2018b`` ``1.54.1`` ``-Python-3.6.6`` ``fosscuda/2018b`` +``1.58.3`` ``-Python-2.7.16`` ``GCCcore/8.3.0`` ``1.60.1`` ``-Python-3.7.2`` ``GCCcore/8.2.0`` +``1.63.1`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` ========== ================== ================================== @@ -10573,6 +11113,7 @@ version versionsuffix toolchain ``1.4.0`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` ``19.8.1`` ``-ASE-3.18.0-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` ``19.8.1`` ``-Python-3.7.2`` ``foss/2019a``, ``intel/2019a`` +``20.1.0`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` ========== ============================ =============================== @@ -10619,14 +11160,15 @@ version toolchain gperftools are for use by developers so that they can create more robust applications. Especially of use to those developing multi-threaded applications in C++ with templates. Includes TCMalloc, heap-checker, heap-profiler and cpu-profiler. -*homepage*: http://github.com/gperftools/gperftools +*homepage*: https://github.com/gperftools/gperftools -========= =============================== -version toolchain -========= =============================== -``2.5`` ``foss/2016a``, ``intel/2016b`` -``2.6.3`` ``GCCcore/6.4.0`` -========= =============================== +========== =============================== +version toolchain +========== =============================== +``2.5`` ``foss/2016a``, ``intel/2016b`` +``2.6.3`` ``GCCcore/6.4.0`` +``2.7.90`` ``GCCcore/8.3.0`` +========== =============================== .. _list_software_gpustat_776: @@ -10652,13 +11194,13 @@ version versionsuffix toolchain Grace is a WYSIWYG tool to make two-dimensional plots of numerical data. -*homepage*: http://plasma-gate.weizmann.ac.il/Grace/ +*homepage*: https://plasma-gate.weizmann.ac.il/Grace/ -========== ============= =============================================== -version versionsuffix toolchain -========== ============= =============================================== -``5.1.25`` ``-5build1`` ``foss/2017b``, ``foss/2018a``, ``intel/2017b`` -========== ============= =============================================== +========== ============= ================================================================================================================= +version versionsuffix toolchain +========== ============= ================================================================================================================= +``5.1.25`` ``-5build1`` ``foss/2017b``, ``foss/2018a``, ``foss/2019a``, ``foss/2019b``, ``intel/2017b``, ``intel/2019a``, ``intel/2019b`` +========== ============= ================================================================================================================= .. _list_software_grace_514: @@ -10690,6 +11232,7 @@ Complete Gradle install. From mobile apps to microservices, from small startups version toolchain ========= ========== ``4.5.1`` ``system`` +``6.1.1`` ``system`` ========= ========== @@ -10749,7 +11292,7 @@ version toolchain GraphicsMagick is the swiss army knife of image processing. -*homepage*: http://www.graphicsmagick.org/ +*homepage*: https://www.graphicsmagick.org/ ========== ================================ version toolchain @@ -10758,9 +11301,26 @@ version toolchain ``1.3.25`` ``intel/2016b``, ``intel/2017a`` ``1.3.28`` ``foss/2018a`` ``1.3.31`` ``foss/2018b`` +``1.3.34`` ``foss/2019a``, ``foss/2019b`` ========== ================================ +.. _list_software_GraphMap2_834: + +*GraphMap2* ++++++++++++ + +A highly sensitive and accurate mapper for long, error-prone reads + +*homepage*: https://github.com/lbcb-sci/graphmap2 + +========= ============== +version toolchain +========= ============== +``0.6.4`` ``foss/2019b`` +========= ============== + + .. _list_software_Graphviz_843: *Graphviz* @@ -10768,14 +11328,17 @@ version toolchain Graphviz is open source graph visualization software. Graph visualization is a way of representing structural information as diagrams of abstract graphs and networks. It has important applications in networking, bioinformatics, software engineering, database and web design, machine learning, and in visual interfaces for other technical domains. -*homepage*: http://www.graphviz.org/ +*homepage*: https://www.graphviz.org/ -========== =============================== -version toolchain -========== =============================== -``2.38.0`` ``foss/2016b``, ``intel/2016b`` -``2.40.1`` ``intel/2018a`` -========== =============================== +========== ================== =============================== +version versionsuffix toolchain +========== ================== =============================== +``2.38.0`` ``foss/2016b``, ``intel/2016b`` +``2.40.1`` ``foss/2018b``, ``intel/2018a`` +``2.40.1`` ``-Python-2.7.15`` ``foss/2018b`` +``2.42.2`` ``foss/2019b`` +``2.42.2`` ``-Python-3.7.4`` ``foss/2019b`` +========== ================== =============================== .. _list_software_graphviz_875: @@ -10796,6 +11359,22 @@ version versionsuffix toolchain ========= ================== =============================== +.. _list_software_GRASP_381: + +*GRASP* ++++++++ + +The General Relativistic Atomic Structure Package (GRASP) is a set of Fortran 90 programs for performing fully-relativistic electron structure calculations of atoms. + +*homepage*: https://compas.github.io/grasp/ + +======== ============== +version toolchain +======== ============== +``2018`` ``foss/2019b`` +======== ============== + + .. _list_software_GRASS_384: *GRASS* @@ -10947,6 +11526,7 @@ version versionsuffix toolchain ``2019.2`` ``fosscuda/2019a`` ``2019.3`` ``foss/2019a``, ``foss/2019b``, ``fosscuda/2019a``, ``fosscuda/2019b`` ``2019.4`` ``foss/2019b`` +``2020`` ``foss/2019b``, ``fosscuda/2019b`` ========== ================= ============================================================================================================ @@ -10982,6 +11562,22 @@ version versionsuffix toolchain ========= ================== ============== +.. _list_software_Groovy_646: + +*Groovy* +++++++++ + +Groovy is a powerful, optionally typed and dynamic language, with static-typing and static compilation capabilities, for the Java platform aimed at improving developer productivity thanks to a concise, familiar and easy to learn syntax. + +*homepage*: https://groovy-lang.org + +========= ============= ========== +version versionsuffix toolchain +========= ============= ========== +``2.5.9`` ``-Java-11`` ``system`` +========= ============= ========== + + .. _list_software_gsettings-desktop-schemas_2576: *gsettings-desktop-schemas* @@ -11029,11 +11625,28 @@ The gSOAP toolkit is a C and C++ software development toolkit for SOAP and REST *homepage*: http://www.cs.fsu.edu/~engelen/soap.html -========== ================= -version toolchain -========== ================= -``2.8.48`` ``GCCcore/6.3.0`` -========== ================= +=========== ================= +version toolchain +=========== ================= +``2.8.48`` ``GCCcore/6.3.0`` +``2.8.100`` ``GCCcore/8.3.0`` +=========== ================= + + +.. _list_software_gsport_671: + +*gsport* +++++++++ + +GSPORT command-line tool for accessing GenomeScan Customer Portal + +*homepage*: https://github.com/genomescan/gsport + +========= ================= ================= +version versionsuffix toolchain +========= ================= ================= +``1.4.2`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` +========= ================= ================= .. _list_software_GST-plugins-base_1509: @@ -11089,6 +11702,7 @@ version versionsuffix toolchain ========= ================== =============================== ``0.2.2`` ``-Python-2.7.15`` ``intel/2018b`` ``0.3.2`` ``-Python-2.7.15`` ``foss/2019a``, ``intel/2019a`` +``1.0.2`` ``-Python-3.7.4`` ``intel/2019b`` ========= ================== =============================== @@ -11101,12 +11715,13 @@ Google's framework for writing C++ tests on a variety of platforms *homepage*: https://github.com/google/googletest -========= ==================================== -version toolchain -========= ==================================== -``1.8.0`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0`` -``1.8.1`` ``GCCcore/8.2.0`` -========= ==================================== +========== ==================================== +version toolchain +========== ==================================== +``1.8.0`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0`` +``1.8.1`` ``GCCcore/8.2.0`` +``1.10.0`` ``GCCcore/8.3.0`` +========== ==================================== .. _list_software_GTK+_273: @@ -11127,6 +11742,7 @@ version toolchain ``2.24.32`` ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``intel/2017b``, ``intel/2018a`` ``3.22.30`` ``fosscuda/2018b`` ``3.24.8`` ``GCCcore/8.2.0`` +``3.24.13`` ``GCCcore/8.3.0`` =========== ================================================================================ @@ -11180,20 +11796,36 @@ version toolchain ============ ================================================================================================================= -.. _list_software_guenomu_768: +.. _list_software_gubbins_746: -*guenomu* +*gubbins* +++++++++ -guenomu is a software written in C that estimates the species tree for a given set of gene families. +Gubbins (Genealogies Unbiased By recomBinations In Nucleotide Sequences) is an algorithm that iteratively identifies loci containing elevated densities of base substitutions while concurrently constructing a phylogeny based on the putative point mutations outside of these regions. Simulations demonstrate the algorithm generates highly accurate reconstructions under realistic models of short-term bacterial evolution, and can be run in only a few hours on alignments of hundreds of bacterial genome sequences. -*homepage*: https://bitbucket.org/leomrtns/guenomu +*homepage*: https://sanger-pathogens.github.io/gubbins -============== ============= =============== -version versionsuffix toolchain -============== ============= =============== -``2019.07.05`` ``-mpi`` ``iimpi/2019a`` -============== ============= =============== +========= ========== +version toolchain +========= ========== +``2.4.0`` ``system`` +========= ========== + + +.. _list_software_guenomu_768: + +*guenomu* ++++++++++ + +guenomu is a software written in C that estimates the species tree for a given set of gene families. + +*homepage*: https://bitbucket.org/leomrtns/guenomu + +============== ============= =============== +version versionsuffix toolchain +============== ============= =============== +``2019.07.05`` ``-mpi`` ``iimpi/2019a`` +============== ============= =============== .. _list_software_Guile_502: @@ -11251,6 +11883,8 @@ version versionsuffix toolchain ``8.1.1`` ``system`` ``9.0.0`` ``system`` ``9.0.0`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` +``9.0.0`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` +``9.0.1`` ``system`` ========= ================= =============================== @@ -11268,7 +11902,7 @@ version toolchain ======== ======================================================= ``1.8`` ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0`` ``1.9`` ``GCCcore/7.3.0`` -``1.10`` ``GCCcore/8.2.0`` +``1.10`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` ======== ======================================================= @@ -11450,6 +12084,7 @@ version toolchain ``1.9.0`` ``fosscuda/2018b`` ``2.2.0`` ``foss/2018b``, ``fosscuda/2018b`` ``2.4.0`` ``GCCcore/8.2.0`` +``2.6.4`` ``GCCcore/8.3.0`` ========= ================================================ @@ -11494,11 +12129,12 @@ HDDM is a Puthon toolbox for hierarchical Bayesian parameter estimation of the *homepage*: http://ski.clps.brown.edu/hddm_docs -========= ================= =============== -version versionsuffix toolchain -========= ================= =============== -``0.6.1`` ``-Python-3.6.6`` ``intel/2018b`` -========= ================= =============== +========= ================== =============== +version versionsuffix toolchain +========= ================== =============== +``0.6.1`` ``-Python-3.6.6`` ``intel/2018b`` +``0.7.5`` ``-Python-2.7.16`` ``intel/2019b`` +========= ================== =============== .. _list_software_HDF_210: @@ -11651,6 +12287,7 @@ version toolchain ``1.47.7`` ``GCCcore/8.2.0`` ``1.47.8`` ``GCCcore/7.4.0``, ``GCCcore/8.3.0`` ``1.47.10`` ``GCCcore/9.1.0``, ``GCCcore/9.2.0`` +``1.47.12`` ``GCCcore/9.3.0`` =========== ================================================================================================================================================================================== @@ -11818,7 +12455,9 @@ version versionsuffix toolchain ``0.9.10`` ``-Python-3.6.3`` ``intel/2017b`` ``0.18.1`` ``-Python-3.7.2`` ``foss/2019a`` ``0.18.2`` ``-TensorFlow-1.15.0-Python-3.7.4`` ``fosscuda/2019b`` +``0.18.2`` ``-TensorFlow-1.15.2-Python-3.7.4`` ``fosscuda/2019b`` ``0.18.2`` ``-TensorFlow-2.0.0-Python-3.7.4`` ``fosscuda/2019b`` +``0.19.1`` ``-TensorFlow-2.1.0-Python-3.7.4`` ``fosscuda/2019b`` ========== =================================== ================== @@ -11969,6 +12608,7 @@ version versionsuffix toolchain ``1.7`` ``intel/2018a`` ``1.8`` ``foss/2018a``, ``intel/2018a`` ``1.9`` ``GCC/6.4.0-2.28``, ``GCC/8.2.0-2.31.1``, ``foss/2018b``, ``iccifort/2017.4.196-GCC-6.4.0-2.28``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``intel/2018b`` +``1.10.2`` ``GCC/8.3.0``, ``iccifort/2019.5.281`` ``20160107`` ``-PacBio`` ``intel/2017a`` ============ ============= =========================================================================================================================================================== @@ -12123,6 +12763,7 @@ version toolchain ``2.11.1`` ``foss/2016a``, ``intel/2016a`` ``2.14.0`` ``foss/2018a``, ``intel/2018a`` ``2.15.1`` ``foss/2019a``, ``intel/2019a`` +``2.18.2`` ``foss/2019b``, ``intel/2019b`` ========== =============================== @@ -12132,7 +12773,7 @@ version toolchain --- -:ref:`list_software_i-cisTarget_1084` - :ref:`list_software_i-PI_303` - :ref:`list_software_I-TASSER_584` - :ref:`list_software_ICA-AROMA_618` - :ref:`list_software_icc_303` - :ref:`list_software_iccifort_851` - :ref:`list_software_iccifortcuda_1264` - :ref:`list_software_icmake_618` - :ref:`list_software_iCount_626` - :ref:`list_software_ICU_225` - :ref:`list_software_IDBA-UD_470` - :ref:`list_software_ieeg-cli_767` - :ref:`list_software_ifort_548` - :ref:`list_software_IGMPlot_636` - :ref:`list_software_igraph_635` - :ref:`list_software_IGV_230` - :ref:`list_software_IGVTools_759` - :ref:`list_software_iimpi_536` - :ref:`list_software_iimpic_635` - :ref:`list_software_IMa2_297` - :ref:`list_software_IMa2p_409` - :ref:`list_software_imageio_731` - :ref:`list_software_ImageJ_557` - :ref:`list_software_ImageMagick_1071` - :ref:`list_software_imake_519` - :ref:`list_software_IMB_216` - :ref:`list_software_imbalanced-learn_1599` - :ref:`list_software_imgaug_634` - :ref:`list_software_imkl_429` - :ref:`list_software_Imlib2_543` - :ref:`list_software_IMOD_297` - :ref:`list_software_impi_431` - :ref:`list_software_IMPUTE2_518` - :ref:`list_software_Inelastica_1021` - :ref:`list_software_Infernal_815` - :ref:`list_software_Infomap_714` - :ref:`list_software_inputproto_1124` - :ref:`list_software_Inspector_951` - :ref:`list_software_IntaRNA_621` - :ref:`list_software_INTEGRATE_675` - :ref:`list_software_INTEGRATE-Neo_1010` - :ref:`list_software_intel_540` - :ref:`list_software_IntelClusterChecker_1939` - :ref:`list_software_intelcuda_953` - :ref:`list_software_IntelPython_1150` - :ref:`list_software_InterProScan_1208` - :ref:`list_software_intltool_885` - :ref:`list_software_io_lib_622` - :ref:`list_software_iomkl_540` - :ref:`list_software_iompi_542` - :ref:`list_software_IOR_234` - :ref:`list_software_IOzone_596` - :ref:`list_software_Ipopt_524` - :ref:`list_software_ipp_329` - :ref:`list_software_IPy_274` - :ref:`list_software_ipyparallel_1183` - :ref:`list_software_ipyrad_649` - :ref:`list_software_IPython_715` - :ref:`list_software_IQ-TREE_503` - :ref:`list_software_IRkernel_796` - :ref:`list_software_IronPython_1050` - :ref:`list_software_ISL_232` - :ref:`list_software_ispc_431` - :ref:`list_software_itac_417` - :ref:`list_software_ITK_232` - :ref:`list_software_ITSTool_654` +:ref:`list_software_i-cisTarget_1084` - :ref:`list_software_i-PI_303` - :ref:`list_software_I-TASSER_584` - :ref:`list_software_ICA-AROMA_618` - :ref:`list_software_icc_303` - :ref:`list_software_iccifort_851` - :ref:`list_software_iccifortcuda_1264` - :ref:`list_software_icmake_618` - :ref:`list_software_iCount_626` - :ref:`list_software_ICU_225` - :ref:`list_software_IDBA-UD_470` - :ref:`list_software_ieeg-cli_767` - :ref:`list_software_ifort_548` - :ref:`list_software_IGMPlot_636` - :ref:`list_software_igraph_635` - :ref:`list_software_IGV_230` - :ref:`list_software_igv-reports_1154` - :ref:`list_software_IGVTools_759` - :ref:`list_software_iimpi_536` - :ref:`list_software_iimpic_635` - :ref:`list_software_IMa2_297` - :ref:`list_software_IMa2p_409` - :ref:`list_software_imageio_731` - :ref:`list_software_ImageJ_557` - :ref:`list_software_ImageMagick_1071` - :ref:`list_software_imake_519` - :ref:`list_software_IMB_216` - :ref:`list_software_imbalanced-learn_1599` - :ref:`list_software_imgaug_634` - :ref:`list_software_imkl_429` - :ref:`list_software_Imlib2_543` - :ref:`list_software_IMOD_297` - :ref:`list_software_impi_431` - :ref:`list_software_IMPUTE2_518` - :ref:`list_software_Inelastica_1021` - :ref:`list_software_inferCNV_763` - :ref:`list_software_Infernal_815` - :ref:`list_software_Infomap_714` - :ref:`list_software_inputproto_1124` - :ref:`list_software_Inspector_951` - :ref:`list_software_IntaRNA_621` - :ref:`list_software_INTEGRATE_675` - :ref:`list_software_INTEGRATE-Neo_1010` - :ref:`list_software_intel_540` - :ref:`list_software_IntelClusterChecker_1939` - :ref:`list_software_intelcuda_953` - :ref:`list_software_IntelPython_1150` - :ref:`list_software_InterProScan_1208` - :ref:`list_software_intltool_885` - :ref:`list_software_io_lib_622` - :ref:`list_software_iomkl_540` - :ref:`list_software_iompi_542` - :ref:`list_software_IOR_234` - :ref:`list_software_IOzone_596` - :ref:`list_software_Ipopt_524` - :ref:`list_software_ipp_329` - :ref:`list_software_IPy_274` - :ref:`list_software_ipyparallel_1183` - :ref:`list_software_ipyrad_649` - :ref:`list_software_IPython_715` - :ref:`list_software_IQ-TREE_503` - :ref:`list_software_IRkernel_796` - :ref:`list_software_IronPython_1050` - :ref:`list_software_ISL_232` - :ref:`list_software_ispc_431` - :ref:`list_software_itac_417` - :ref:`list_software_ITK_232` - :ref:`list_software_ITSTool_654` - :ref:`list_software_iVar_402` .. _list_software_i-cisTarget_1084: @@ -12280,6 +12921,7 @@ version versionsuffix toolchain ``2019.4.243`` ``system`` ``2019.5.281`` ``system`` ``2020.0.166`` ``system`` +``2020.0.166`` ``-GCC-9.2.0`` ``system`` ``system`` ``-GCC-system-2.29`` ``system`` ============== ===================== ========== @@ -12449,12 +13091,13 @@ version toolchain igraph is a collection of network analysis tools with the emphasis on efficiency, portability and ease of use. igraph is open source and free. igraph can be programmed in R, Python and C/C++. -*homepage*: http://igraph.org +*homepage*: https://igraph.org ========= ================================================ version toolchain ========= ================================================ ``0.7.1`` ``foss/2018b``, ``intel/2016b``, ``intel/2017b`` +``0.8.0`` ``foss/2019b`` ========= ================================================ @@ -12465,7 +13108,7 @@ version toolchain This package contains command line utilities for preprocessing, computing feature count density (coverage), sorting, and indexing data files. -*homepage*: http://www.broadinstitute.org/software/igv/ +*homepage*: https://www.broadinstitute.org/software/igv/ ========== ================== ========== version versionsuffix toolchain @@ -12473,9 +13116,26 @@ version versionsuffix toolchain ``2.3.68`` ``-Java-1.7.0_80`` ``system`` ``2.3.80`` ``-Java-1.7.0_80`` ``system`` ``2.5.0`` ``-Java-11`` ``system`` +``2.8.0`` ``-Java-11`` ``system`` ========== ================== ========== +.. _list_software_igv-reports_1154: + +*igv-reports* ++++++++++++++ + +Python application to generate self-contained igv.js pages that can be opened within a browser with "file" protocol. + +*homepage*: https://github.com/igvteam/igv-reports + +========= ================= ============= +version versionsuffix toolchain +========= ================= ============= +``0.9.8`` ``-Python-3.7.4`` ``GCC/8.3.0`` +========= ================= ============= + + .. _list_software_IGVTools_759: *IGVTools* @@ -12836,7 +13496,7 @@ version versionsuffix toolchain ``2019.1.144`` ``iccifort/2019.1.144-GCC-8.2.0-2.31.1`` ``2019.2.187`` ``iccifort/2019.2.187-GCC-8.2.0-2.31.1`` ``2019.3.199`` ``iccifort/2019.3.199-GCC-8.3.0-2.32`` -``2019.6.166`` ``iccifort/2020.0.166`` +``2019.6.166`` ``iccifort/2020.0.166-GCC-9.2.0`` ``system`` ``iccifort/system-GCC-system-2.29`` ============== ============= ================================================================================================================================================================================================================================ @@ -12876,6 +13536,22 @@ version versionsuffix toolchain ========= ================== =============== +.. _list_software_inferCNV_763: + +*inferCNV* +++++++++++ + +InferCNV is used to explore tumor single cell RNA-Seq data to identify evidence for somatic large-scale chromosomal copy number alterations, such as gains or deletions of entire chromosomes or large segments of chromosomes. + +*homepage*: https://github.com/broadinstitute/inferCNV/wiki + +========= ========================= ============== +version versionsuffix toolchain +========= ========================= ============== +``1.0.4`` ``-Python-3.7.2-R-3.6.0`` ``foss/2019a`` +========= ========================= ============== + + .. _list_software_Infernal_815: *Infernal* @@ -13346,7 +14022,7 @@ version versionsuffix toolchain ``6.4.0`` ``-Python-3.6.4`` ``foss/2018a`` ``7.2.0`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b`` ``7.7.0`` ``-Python-3.7.2`` ``foss/2019a``, ``fosscuda/2019a``, ``intel/2019a`` -``7.9.0`` ``-Python-3.7.4`` ``foss/2019b`` +``7.9.0`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b`` ========= ================== ======================================================================================= @@ -13359,12 +14035,13 @@ Efficient phylogenomic software by maximum likelihood *homepage*: http://www.iqtree.org/ -========= ============= =============== -version versionsuffix toolchain -========= ============= =============== -``1.5.5`` ``-omp-mpi`` ``foss/2016a`` -``1.6.6`` ``intel/2018a`` -========= ============= =============== +========== ============= =============== +version versionsuffix toolchain +========== ============= =============== +``1.5.5`` ``-omp-mpi`` ``foss/2016a`` +``1.6.6`` ``intel/2018a`` +``1.6.12`` ``intel/2019b`` +========== ============= =============== .. _list_software_IRkernel_796: @@ -13376,11 +14053,12 @@ The R kernel for the 'Jupyter' environment executes R code which the front-end *homepage*: https://irkernel.github.io -========== ========================== =============================== -version versionsuffix toolchain -========== ========================== =============================== -``0.8.15`` ``-R-3.4.3-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` -========== ========================== =============================== +========== ========================== ================================== +version versionsuffix toolchain +========== ========================== ================================== +``0.8.15`` ``-R-3.4.3-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` +``1.1`` ``-R-3.6.2-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` +========== ========================== ================================== .. _list_software_IronPython_1050: @@ -13432,6 +14110,7 @@ version toolchain ========== ========== ``1.6.0`` ``system`` ``1.10.0`` ``system`` +``1.12.0`` ``system`` ========== ========== @@ -13477,6 +14156,7 @@ version versionsuffix toolchain ``4.13.1`` ``-Python-3.6.4`` ``foss/2018a`` ``4.13.1`` ``-Python-3.6.6`` ``foss/2018b`` ``5.0.1`` ``-Python-3.7.2`` ``foss/2019a`` +``5.0.1`` ``-Python-3.7.4`` ``foss/2019b`` ``5.0b01`` ``-Python-3.6.6`` ``foss/2018b`` ========== ================== ============== @@ -13499,13 +14179,29 @@ version versionsuffix toolchain ========= ================== ================= +.. _list_software_iVar_402: + +*iVar* +++++++ + +iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing. + +*homepage*: https://github.com/andersen-lab/ivar + +========= ============== +version toolchain +========= ============== +``1.0.1`` ``foss/2018b`` +========= ============== + + .. _list_software_letter_j: *J* --- -:ref:`list_software_JAGS_293` - :ref:`list_software_Jansson_732` - :ref:`list_software_JasPer_581` - :ref:`list_software_Java_386` - :ref:`list_software_JAXFrontCE_884` - :ref:`list_software_jbigkit_740` - :ref:`list_software_Jellyfish_938` - :ref:`list_software_jemalloc_839` - :ref:`list_software_jhbuild_738` - :ref:`list_software_JiTCODE_546` - :ref:`list_software_jModelTest_1019` - :ref:`list_software_jq_219` - :ref:`list_software_JsonCpp_701` - :ref:`list_software_JUBE_294` - :ref:`list_software_Judy_412` - :ref:`list_software_Julia_501` - :ref:`list_software_JUnit_490` - :ref:`list_software_jupyterhub_1106` - :ref:`list_software_JWM_238` +:ref:`list_software_JAGS_293` - :ref:`list_software_Jansson_732` - :ref:`list_software_JasPer_581` - :ref:`list_software_Java_386` - :ref:`list_software_JAXFrontCE_884` - :ref:`list_software_jbigkit_740` - :ref:`list_software_Jellyfish_938` - :ref:`list_software_jemalloc_839` - :ref:`list_software_jhbuild_738` - :ref:`list_software_JiTCODE_546` - :ref:`list_software_jModelTest_1019` - :ref:`list_software_joypy_571` - :ref:`list_software_jq_219` - :ref:`list_software_JsonCpp_701` - :ref:`list_software_JUBE_294` - :ref:`list_software_Judy_412` - :ref:`list_software_Julia_501` - :ref:`list_software_JUnit_490` - :ref:`list_software_jupyterhub_1106` - :ref:`list_software_JupyterLab_1026` - :ref:`list_software_JWM_238` .. _list_software_JAGS_293: @@ -13517,12 +14213,12 @@ JAGS is Just Another Gibbs Sampler. It is a program for analysis of Bayesian *homepage*: http://mcmc-jags.sourceforge.net/ -========= ================================================ -version toolchain -========= ================================================ -``4.2.0`` ``foss/2016a``, ``intel/2016a``, ``intel/2017a`` -``4.3.0`` ``foss/2017b``, ``foss/2018b``, ``intel/2017b`` -========= ================================================ +========= =============================================================== +version toolchain +========= =============================================================== +``4.2.0`` ``foss/2016a``, ``intel/2016a``, ``intel/2017a`` +``4.3.0`` ``foss/2017b``, ``foss/2018b``, ``foss/2019a``, ``intel/2017b`` +========= =============================================================== .. _list_software_Jansson_732: @@ -13567,54 +14263,58 @@ version toolchain Java Platform, Standard Edition (Java SE) lets you develop and deploy Java applications on desktops and servers. -*homepage*: http://java.com/ - -======================= ========== -version toolchain -======================= ========== -``1.6.0_24`` ``system`` -``1.7.0_10`` ``system`` -``1.7.0_15`` ``system`` -``1.7.0_21`` ``system`` -``1.7.0_40`` ``system`` -``1.7.0_45`` ``system`` -``1.7.0_60`` ``system`` -``1.7.0_75`` ``system`` -``1.7.0_76`` ``system`` -``1.7.0_79`` ``system`` -``1.7.0_80`` ``system`` -``1.8`` ``system`` -``1.8.0_20`` ``system`` -``1.8.0_25`` ``system`` -``1.8.0_31`` ``system`` -``1.8.0_40`` ``system`` -``1.8.0_45`` ``system`` -``1.8.0_60`` ``system`` -``1.8.0_65`` ``system`` -``1.8.0_66`` ``system`` -``1.8.0_72`` ``system`` -``1.8.0_74`` ``system`` -``1.8.0_77`` ``system`` -``1.8.0_92`` ``system`` -``1.8.0_112`` ``system`` -``1.8.0_121`` ``system`` -``1.8.0_131`` ``system`` -``1.8.0_141`` ``system`` -``1.8.0_144`` ``system`` -``1.8.0_152`` ``system`` -``1.8.0_162`` ``system`` -``1.8.0_172`` ``system`` -``1.8.0_181`` ``system`` -``1.8.0_192`` ``system`` -``1.8.0_202`` ``system`` -``1.8.0_212`` ``system`` -``1.8.0_221`` ``system`` -``1.8.0_231`` ``system`` -``1.8_191-b26-OpenJDK`` ``system`` -``1.9.0.4`` ``system`` -``11`` ``system`` -``11.0.2`` ``system`` -======================= ========== +*homepage*: https://java.com/ + +======================= ============= ========== +version versionsuffix toolchain +======================= ============= ========== +``1.6.0_24`` ``system`` +``1.7.0_10`` ``system`` +``1.7.0_15`` ``system`` +``1.7.0_21`` ``system`` +``1.7.0_40`` ``system`` +``1.7.0_45`` ``system`` +``1.7.0_60`` ``system`` +``1.7.0_75`` ``system`` +``1.7.0_76`` ``system`` +``1.7.0_79`` ``system`` +``1.7.0_80`` ``system`` +``1.8`` ``system`` +``1.8.0_20`` ``system`` +``1.8.0_25`` ``system`` +``1.8.0_31`` ``system`` +``1.8.0_40`` ``system`` +``1.8.0_45`` ``system`` +``1.8.0_60`` ``system`` +``1.8.0_65`` ``system`` +``1.8.0_66`` ``system`` +``1.8.0_72`` ``system`` +``1.8.0_74`` ``system`` +``1.8.0_77`` ``system`` +``1.8.0_92`` ``system`` +``1.8.0_112`` ``system`` +``1.8.0_121`` ``system`` +``1.8.0_131`` ``system`` +``1.8.0_141`` ``system`` +``1.8.0_144`` ``system`` +``1.8.0_152`` ``system`` +``1.8.0_162`` ``system`` +``1.8.0_172`` ``system`` +``1.8.0_181`` ``system`` +``1.8.0_192`` ``system`` +``1.8.0_202`` ``system`` +``1.8.0_212`` ``system`` +``1.8.0_221`` ``system`` +``1.8.0_231`` ``system`` +``1.8.0_241`` ``system`` +``1.8_191-b26-OpenJDK`` ``system`` +``1.9.0.4`` ``system`` +``11`` ``system`` +``11.0.2`` ``system`` +``11.0.6`` ``-ppc64le`` ``system`` +``13`` ``system`` +``13.0.2`` ``system`` +======================= ============= ========== .. _list_software_JAXFrontCE_884: @@ -13658,15 +14358,15 @@ Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA. *homepage*: http://www.genome.umd.edu/jellyfish.html -========== =============================== -version toolchain -========== =============================== -``1.1.11`` ``foss/2016a``, ``foss/2016b`` -``1.1.12`` ``foss/2018b``, ``intel/2018a`` -``2.2.6`` ``foss/2016b``, ``intel/2017a`` -``2.2.10`` ``foss/2018b``, ``intel/2018a`` -``2.3.0`` ``GCC/8.2.0-2.31.1`` -========== =============================== +========== =================================== +version toolchain +========== =================================== +``1.1.11`` ``foss/2016a``, ``foss/2016b`` +``1.1.12`` ``foss/2018b``, ``intel/2018a`` +``2.2.6`` ``foss/2016b``, ``intel/2017a`` +``2.2.10`` ``foss/2018b``, ``intel/2018a`` +``2.3.0`` ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0`` +========== =================================== .. _list_software_jemalloc_839: @@ -13741,6 +14441,22 @@ version versionsuffix toolchain =================== ================== ========== +.. _list_software_joypy_571: + +*joypy* ++++++++ + +Joyplots in Python with matplotlib & pandas + +*homepage*: https://github.com/sbebo/joypy + +========= ================= =============== +version versionsuffix toolchain +========= ================= =============== +``0.2.2`` ``-Python-3.7.4`` ``intel/2019b`` +========= ================= =============== + + .. _list_software_jq_219: *jq* @@ -13822,6 +14538,7 @@ version versionsuffix toolchain ``1.1.1`` ``-linux-x86_64`` ``system`` ``1.2.0`` ``-linux-x86_64`` ``system`` ``1.3.1`` ``-linux-x86_64`` ``system`` +``1.4.0`` ``-linux-x86_64`` ``system`` ========= ================= ========== @@ -13875,6 +14592,22 @@ version versionsuffix toolchain ========= ================= ============== +.. _list_software_JupyterLab_1026: + +*JupyterLab* +++++++++++++ + +JupyterLab is the next-generation user interface for Project Jupyter offering all the familiar building blocks of the classic Jupyter Notebook (notebook, terminal, text editor, file browser, rich outputs, etc.) in a flexible and powerful user interface. JupyterLab will eventually replace the classic Jupyter Notebook. + +*homepage*: https://jupyter.org/ + +========= ================= ================================== +version versionsuffix toolchain +========= ================= ================================== +``1.2.5`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` +========= ================= ================================== + + .. _list_software_JWM_238: *JWM* @@ -13897,7 +14630,7 @@ version toolchain --- -:ref:`list_software_Kaiju_500` - :ref:`list_software_kallisto_867` - :ref:`list_software_KAT_224` - :ref:`list_software_kbproto_769` - :ref:`list_software_Kent_tools_1058` - :ref:`list_software_Keras_502` - :ref:`list_software_khmer_535` - :ref:`list_software_kim-api_680` - :ref:`list_software_KMC_219` - :ref:`list_software_KmerGenie_887` - :ref:`list_software_KNIME_372` - :ref:`list_software_kpcalg_626` - :ref:`list_software_Kraken_604` - :ref:`list_software_Kraken2_654` - :ref:`list_software_Kratos_628` - :ref:`list_software_KronaTools_1036` - :ref:`list_software_kwant_549` - :ref:`list_software_KWIML_388` - :ref:`list_software_kWIP_347` - :ref:`list_software_KyotoCabinet_1228` +:ref:`list_software_Kaiju_500` - :ref:`list_software_kallisto_867` - :ref:`list_software_KAT_224` - :ref:`list_software_kbproto_769` - :ref:`list_software_Kent_tools_1058` - :ref:`list_software_Keras_502` - :ref:`list_software_khmer_535` - :ref:`list_software_kim-api_680` - :ref:`list_software_kma_313` - :ref:`list_software_KMC_219` - :ref:`list_software_KmerGenie_887` - :ref:`list_software_KNIME_372` - :ref:`list_software_kpcalg_626` - :ref:`list_software_Kraken_604` - :ref:`list_software_Kraken2_654` - :ref:`list_software_Kratos_628` - :ref:`list_software_KronaTools_1036` - :ref:`list_software_kwant_549` - :ref:`list_software_KWIML_388` - :ref:`list_software_kWIP_347` - :ref:`list_software_KyotoCabinet_1228` .. _list_software_Kaiju_500: @@ -13914,6 +14647,7 @@ version versionsuffix toolchain ========= ================= =============== ``1.5.0`` ``intel/2016b`` ``1.7.2`` ``-Python-3.7.2`` ``iimpi/2019a`` +``1.7.3`` ``-Python-3.7.4`` ``gompi/2019b`` ========= ================= =============== @@ -13924,7 +14658,7 @@ version versionsuffix toolchain kallisto is a program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. -*homepage*: http://pachterlab.github.io/kallisto/ +*homepage*: https://pachterlab.github.io/kallisto/ ========== ================================================ version toolchain @@ -13936,6 +14670,7 @@ version toolchain ``0.45.0`` ``foss/2018b`` ``0.45.1`` ``foss/2019a`` ``0.46.0`` ``intel/2019a`` +``0.46.1`` ``foss/2019b`` ========== ================================================ @@ -14021,6 +14756,7 @@ version versionsuffix toolchain ``2.2.4`` ``-Python-3.6.4`` ``intel/2018a`` ``2.2.4`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b`` ``2.2.4`` ``-Python-3.7.2`` ``foss/2019a``, ``fosscuda/2019a`` +``2.3.1`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` ========= ================== ================================== @@ -14054,9 +14790,26 @@ Open Knowledgebase of Interatomic Models. KIM is an API and OpenKIM is a collec version toolchain ========= =============================== ``2.1.2`` ``foss/2019a``, ``intel/2019a`` +``2.1.3`` ``foss/2019b``, ``intel/2019b`` ========= =============================== +.. _list_software_kma_313: + +*kma* ++++++ + +KMA is a mapping method designed to map raw reads directly against redundant databases, in an ultra-fast manner using seed and extend. + +*homepage*: https://bitbucket.org/genomicepidemiology/kma + +========== =============== +version toolchain +========== =============== +``1.2.22`` ``intel/2019b`` +========== =============== + + .. _list_software_KMC_219: *KMC* @@ -14152,12 +14905,13 @@ Kraken is a system for assigning taxonomic labels to short DNA sequences, usual *homepage*: http://www.ccb.jhu.edu/software/kraken2/ -============== ================ ============== -version versionsuffix toolchain -============== ================ ============== -``2.0.6-beta`` ``-Perl-5.26.1`` ``foss/2018a`` -``2.0.7-beta`` ``-Perl-5.28.0`` ``foss/2018b`` -============== ================ ============== +============== ================ =============== +version versionsuffix toolchain +============== ================ =============== +``2.0.6-beta`` ``-Perl-5.26.1`` ``foss/2018a`` +``2.0.7-beta`` ``-Perl-5.28.0`` ``foss/2018b`` +``2.0.8-beta`` ``-Perl-5.30.0`` ``gompi/2019b`` +============== ================ =============== .. _list_software_Kratos_628: @@ -14263,7 +15017,7 @@ version toolchain --- -:ref:`list_software_L_RNA_scaffolder_1540` - :ref:`list_software_LAME_287` - :ref:`list_software_LAST_308` - :ref:`list_software_LASTZ_398` - :ref:`list_software_lavaan_627` - :ref:`list_software_LCov_372` - :ref:`list_software_LeadIT_531` - :ref:`list_software_LEMON_379` - :ref:`list_software_Leptonica_927` - :ref:`list_software_less_439` - :ref:`list_software_LevelDB_638` - :ref:`list_software_lftp_438` - :ref:`list_software_libaio_624` - :ref:`list_software_libarchive_1049` - :ref:`list_software_libbitmask_1058` - :ref:`list_software_libcerf_727` - :ref:`list_software_libcircle_937` - :ref:`list_software_libcmaes_832` - :ref:`list_software_libconfig_941` - :ref:`list_software_libcpuset_971` - :ref:`list_software_libcroco_845` - :ref:`list_software_libctl_634` - :ref:`list_software_libdap_620` - :ref:`list_software_libdrm_634` - :ref:`list_software_libdwarf_843` - :ref:`list_software_libedit_733` - :ref:`list_software_libelf_622` - :ref:`list_software_libepoxy_876` - :ref:`list_software_libevent_857` - :ref:`list_software_libffcall_927` - :ref:`list_software_libffi_620` - :ref:`list_software_libFLAME_668` - :ref:`list_software_libfontenc_1060` - :ref:`list_software_libgcrypt_976` - :ref:`list_software_libgd_514` - :ref:`list_software_libgeotiff_1051` - :ref:`list_software_libglade_820` - :ref:`list_software_libGLU_543` - :ref:`list_software_libglvnd_850` - :ref:`list_software_libgpg-error_1228` - :ref:`list_software_libgpuarray_1186` - :ref:`list_software_libgtextutils_1428` - :ref:`list_software_libharu_743` - :ref:`list_software_libibmad_820` - :ref:`list_software_libibumad_937` - :ref:`list_software_libICE_520` - :ref:`list_software_libiconv_854` - :ref:`list_software_libidn_626` - :ref:`list_software_Libint_610` - :ref:`list_software_libjpeg-turbo_1334` - :ref:`list_software_libmatheval_1161` - :ref:`list_software_libmaus2_799` - :ref:`list_software_libMemcached_1198` - :ref:`list_software_libpciaccess_1253` - :ref:`list_software_libpng_636` - :ref:`list_software_libpsl_646` - :ref:`list_software_libpsml_755` - :ref:`list_software_libpsortb_977` - :ref:`list_software_libpthread-stubs_1661` - :ref:`list_software_libQGLViewer_1165` - :ref:`list_software_libreadline_1147` - :ref:`list_software_libRmath_819` - :ref:`list_software_librsvg_761` - :ref:`list_software_libsamplerate_1381` - :ref:`list_software_libsigc++_819` - :ref:`list_software_libsigsegv_1071` - :ref:`list_software_libSM_471` - :ref:`list_software_libsndfile_1052` - :ref:`list_software_libsodium_968` - :ref:`list_software_LibSoup_702` - :ref:`list_software_libspatialindex_1597` - :ref:`list_software_libspatialite_1383` - :ref:`list_software_libssh_645` - :ref:`list_software_LIBSVM_461` - :ref:`list_software_libtar_638` - :ref:`list_software_libtasn1_798` - :ref:`list_software_LibTIFF_576` - :ref:`list_software_libtirpc_857` - :ref:`list_software_libtool_757` - :ref:`list_software_libunistring_1306` - :ref:`list_software_libunwind_972` - :ref:`list_software_libutempter_1197` - :ref:`list_software_LibUUID_590` - :ref:`list_software_libvdwxc_867` - :ref:`list_software_libwebp_741` - :ref:`list_software_libX11_497` - :ref:`list_software_libXau_613` - :ref:`list_software_libxc_530` - :ref:`list_software_libxcb_628` - :ref:`list_software_libXcursor_1069` - :ref:`list_software_libXdamage_1006` - :ref:`list_software_libXdmcp_819` - :ref:`list_software_libXext_736` - :ref:`list_software_libXfixes_942` - :ref:`list_software_libXfont_838` - :ref:`list_software_libXft_617` - :ref:`list_software_libXi_504` - :ref:`list_software_libXinerama_1132` - :ref:`list_software_libxkbcommon_1285` - :ref:`list_software_libxml++_734` - :ref:`list_software_libxml2_698` - :ref:`list_software_libxml2-python_1417` - :ref:`list_software_libXmu_625` - :ref:`list_software_libXp_511` - :ref:`list_software_libXpm_620` - :ref:`list_software_libXrandr_934` - :ref:`list_software_libXrender_1039` - :ref:`list_software_libxslt_770` - :ref:`list_software_libxsmm_764` - :ref:`list_software_libXt_515` - :ref:`list_software_libXxf86vm_958` - :ref:`list_software_libyaml_746` - :ref:`list_software_libzip_650` - :ref:`list_software_lifelines_955` - :ref:`list_software_Lighter_719` - :ref:`list_software_likwid_644` - :ref:`list_software_LinBox_588` - :ref:`list_software_LittleCMS_849` - :ref:`list_software_LLVM_315` - :ref:`list_software_LMDB_287` - :ref:`list_software_LMfit_476` - :ref:`list_software_Lmod_396` - :ref:`list_software_LocARNA_576` - :ref:`list_software_LoFreq_585` - :ref:`list_software_Log-Log4perl_1112` - :ref:`list_software_LOHHLA_440` - :ref:`list_software_Loki_399` - :ref:`list_software_Longshot_846` - :ref:`list_software_lpsolve_773` - :ref:`list_software_lrslib_648` - :ref:`list_software_LS-PrePost_921` - :ref:`list_software_LSMS_319` - :ref:`list_software_Lua_290` - :ref:`list_software_LuaJIT_521` - :ref:`list_software_Lucene-Geo-Gazetteer_1916` - :ref:`list_software_LUMPY_407` - :ref:`list_software_LUSCUS_479` - :ref:`list_software_lwgrp_556` - :ref:`list_software_lxml_445` - :ref:`list_software_lynx_459` - :ref:`list_software_lz4_282` - :ref:`list_software_LZO_245` +:ref:`list_software_L_RNA_scaffolder_1540` - :ref:`list_software_LAME_287` - :ref:`list_software_LAMMPS_458` - :ref:`list_software_lancet_631` - :ref:`list_software_LAST_308` - :ref:`list_software_LASTZ_398` - :ref:`list_software_lavaan_627` - :ref:`list_software_LCov_372` - :ref:`list_software_LeadIT_531` - :ref:`list_software_LEMON_379` - :ref:`list_software_Leptonica_927` - :ref:`list_software_less_439` - :ref:`list_software_LevelDB_638` - :ref:`list_software_lftp_438` - :ref:`list_software_libaio_624` - :ref:`list_software_libarchive_1049` - :ref:`list_software_libBigWig_880` - :ref:`list_software_libbitmask_1058` - :ref:`list_software_libcerf_727` - :ref:`list_software_libcircle_937` - :ref:`list_software_libcmaes_832` - :ref:`list_software_libconfig_941` - :ref:`list_software_libcpuset_971` - :ref:`list_software_libcroco_845` - :ref:`list_software_libctl_634` - :ref:`list_software_libdap_620` - :ref:`list_software_libdrm_634` - :ref:`list_software_libdwarf_843` - :ref:`list_software_libedit_733` - :ref:`list_software_libelf_622` - :ref:`list_software_libepoxy_876` - :ref:`list_software_libevent_857` - :ref:`list_software_libffcall_927` - :ref:`list_software_libffi_620` - :ref:`list_software_libFLAME_668` - :ref:`list_software_libfontenc_1060` - :ref:`list_software_libgcrypt_976` - :ref:`list_software_libgd_514` - :ref:`list_software_libgeotiff_1051` - :ref:`list_software_libglade_820` - :ref:`list_software_libGLU_543` - :ref:`list_software_libglvnd_850` - :ref:`list_software_libgpg-error_1228` - :ref:`list_software_libgpuarray_1186` - :ref:`list_software_libGridXC_856` - :ref:`list_software_libgtextutils_1428` - :ref:`list_software_libharu_743` - :ref:`list_software_libibmad_820` - :ref:`list_software_libibumad_937` - :ref:`list_software_libICE_520` - :ref:`list_software_libiconv_854` - :ref:`list_software_libidn_626` - :ref:`list_software_Libint_610` - :ref:`list_software_libjpeg-turbo_1334` - :ref:`list_software_libmatheval_1161` - :ref:`list_software_libmaus2_799` - :ref:`list_software_libMemcached_1198` - :ref:`list_software_libpciaccess_1253` - :ref:`list_software_libpng_636` - :ref:`list_software_libpsl_646` - :ref:`list_software_libpsml_755` - :ref:`list_software_libPSML_627` - :ref:`list_software_libpsortb_977` - :ref:`list_software_libpthread-stubs_1661` - :ref:`list_software_libQGLViewer_1165` - :ref:`list_software_libreadline_1147` - :ref:`list_software_libRmath_819` - :ref:`list_software_librsvg_761` - :ref:`list_software_libsamplerate_1381` - :ref:`list_software_libsigc++_819` - :ref:`list_software_libsigsegv_1071` - :ref:`list_software_libSM_471` - :ref:`list_software_libsndfile_1052` - :ref:`list_software_libsodium_968` - :ref:`list_software_LibSoup_702` - :ref:`list_software_libspatialindex_1597` - :ref:`list_software_libspatialite_1383` - :ref:`list_software_libssh_645` - :ref:`list_software_LIBSVM_461` - :ref:`list_software_libtar_638` - :ref:`list_software_libtasn1_798` - :ref:`list_software_LibTIFF_576` - :ref:`list_software_libtirpc_857` - :ref:`list_software_libtool_757` - :ref:`list_software_libunistring_1306` - :ref:`list_software_libunwind_972` - :ref:`list_software_libutempter_1197` - :ref:`list_software_LibUUID_590` - :ref:`list_software_libvdwxc_867` - :ref:`list_software_libwebp_741` - :ref:`list_software_libX11_497` - :ref:`list_software_libXau_613` - :ref:`list_software_libxc_530` - :ref:`list_software_libxcb_628` - :ref:`list_software_libXcursor_1069` - :ref:`list_software_libXdamage_1006` - :ref:`list_software_libXdmcp_819` - :ref:`list_software_libXext_736` - :ref:`list_software_libXfixes_942` - :ref:`list_software_libXfont_838` - :ref:`list_software_libXft_617` - :ref:`list_software_libXi_504` - :ref:`list_software_libXinerama_1132` - :ref:`list_software_libxkbcommon_1285` - :ref:`list_software_libxml++_734` - :ref:`list_software_libxml2_698` - :ref:`list_software_libxml2-python_1417` - :ref:`list_software_libXmu_625` - :ref:`list_software_libXp_511` - :ref:`list_software_libXpm_620` - :ref:`list_software_libXrandr_934` - :ref:`list_software_libXrender_1039` - :ref:`list_software_libxslt_770` - :ref:`list_software_libxsmm_764` - :ref:`list_software_libXt_515` - :ref:`list_software_libXxf86vm_958` - :ref:`list_software_libyaml_746` - :ref:`list_software_libzip_650` - :ref:`list_software_lifelines_955` - :ref:`list_software_Lighter_719` - :ref:`list_software_likwid_644` - :ref:`list_software_LinBox_588` - :ref:`list_software_LittleCMS_849` - :ref:`list_software_LLVM_315` - :ref:`list_software_LMDB_287` - :ref:`list_software_LMfit_476` - :ref:`list_software_Lmod_396` - :ref:`list_software_LocARNA_576` - :ref:`list_software_LoFreq_585` - :ref:`list_software_Log-Log4perl_1112` - :ref:`list_software_LOHHLA_440` - :ref:`list_software_Loki_399` - :ref:`list_software_Longshot_846` - :ref:`list_software_lpsolve_773` - :ref:`list_software_lrslib_648` - :ref:`list_software_LS-PrePost_921` - :ref:`list_software_LSMS_319` - :ref:`list_software_LtrDetector_1132` - :ref:`list_software_Lua_290` - :ref:`list_software_LuaJIT_521` - :ref:`list_software_Lucene-Geo-Gazetteer_1916` - :ref:`list_software_LUMPY_407` - :ref:`list_software_LUSCUS_479` - :ref:`list_software_lwgrp_556` - :ref:`list_software_lxml_445` - :ref:`list_software_lynx_459` - :ref:`list_software_lz4_282` - :ref:`list_software_LZO_245` .. _list_software_L_RNA_scaffolder_1540: @@ -14299,6 +15053,39 @@ version toolchain ========== =========================================================================================== +.. _list_software_LAMMPS_458: + +*LAMMPS* +++++++++ + +LAMMPS is a classical molecular dynamics code, and an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator. LAMMPS has potentials for solid-state materials (metals, semiconductors) and soft matter (biomolecules, polymers) and coarse-grained or mesoscopic systems. It can be used to model atoms or, more generically, as a parallel particle simulator at the atomic, meso, or continuum scale. LAMMPS runs on single processors or in parallel using message-passing techniques and a spatial-decomposition of the simulation domain. The code is designed to be easy to modify or extend with new functionality. + +*homepage*: https://lammps.sandia.gov/ + +============ ======================== =============================== +version versionsuffix toolchain +============ ======================== =============================== +``3Mar2020`` ``-Python-3.7.4-kokkos`` ``foss/2019b``, ``intel/2019b`` +``7Aug2019`` ``-Python-3.7.4-kokkos`` ``foss/2019b``, ``intel/2019b`` +============ ======================== =============================== + + +.. _list_software_lancet_631: + +*lancet* +++++++++ + +Lancet is a somatic variant caller (SNVs and indels) for short read data. + +*homepage*: https://github.com/nygenome/lancet + +========= ======================= +version toolchain +========= ======================= +``1.1.0`` ``iccifort/2019.5.281`` +========= ======================= + + .. _list_software_LAST_308: *LAST* @@ -14308,12 +15095,13 @@ LAST finds similar regions between sequences. *homepage*: http://last.cbrc.jp/ -======= =============== -version toolchain -======= =============== -``869`` ``intel/2017a`` -``914`` ``intel/2017b`` -======= =============== +======== =============== +version toolchain +======== =============== +``869`` ``intel/2017a`` +``914`` ``intel/2017b`` +``1045`` ``intel/2019b`` +======== =============== .. _list_software_LASTZ_398: @@ -14323,12 +15111,13 @@ version toolchain LASTZ is a program for aligning DNA sequences, a pairwise aligner. Originally designed to handle sequences the size of human chromosomes and from different species, it is also useful for sequences produced by NGS sequencing technologies such as Roche 454. -*homepage*: http://www.bx.psu.edu/~rsharris/lastz/ +*homepage*: https://www.bx.psu.edu/~rsharris/lastz/ =========== ============== version toolchain =========== ============== ``1.02.00`` ``foss/2016a`` +``1.04.03`` ``foss/2019b`` =========== ============== @@ -14496,6 +15285,22 @@ version toolchain ========= ================= +.. _list_software_libBigWig_880: + +*libBigWig* ++++++++++++ + +A C library for handling bigWig files + +*homepage*: https://github.com/dpryan79/libBigWig + +========= ================= +version toolchain +========= ================= +``0.4.4`` ``GCCcore/8.3.0`` +========= ================= + + .. _list_software_libbitmask_1058: *libbitmask* @@ -14657,7 +15462,7 @@ version versionsuffix toolchain Direct Rendering Manager runtime library. -*homepage*: http://dri.freedesktop.org +*homepage*: https://dri.freedesktop.org ========== ================================================== version toolchain @@ -14738,6 +15543,7 @@ Epoxy is a library for handling OpenGL function pointer management for you version toolchain ========= ===================================== ``1.5.3`` ``GCCcore/8.2.0``, ``fosscuda/2018b`` +``1.5.4`` ``GCCcore/8.3.0`` ========= ===================================== @@ -14750,13 +15556,13 @@ The libevent API provides a mechanism to execute a callback function when a spec *homepage*: http://libevent.org/ -========== ======================================================================== -version toolchain -========== ======================================================================== -``2.0.22`` ``GCC/4.9.2``, ``GCC/5.4.0-2.26``, ``GCCcore/4.9.3``, ``GNU/4.9.3-2.25`` -``2.1.8`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``system`` -``2.1.11`` ``GCCcore/8.3.0`` -========== ======================================================================== +========== ====================================================================================== +version toolchain +========== ====================================================================================== +``2.0.22`` ``GCC/4.9.2``, ``GCC/5.4.0-2.26``, ``GCCcore/4.9.3``, ``GNU/4.9.3-2.25`` +``2.1.8`` ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``system`` +``2.1.11`` ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.3.0`` +========== ====================================================================================== .. _list_software_libffcall_927: @@ -14961,9 +15767,26 @@ version versionsuffix toolchain ``0.7.6`` ``fosscuda/2019a`` ``0.7.6`` ``-Python-2.7.15`` ``fosscuda/2018b`` ``0.7.6`` ``-Python-3.6.6`` ``fosscuda/2018b`` +``0.7.6`` ``-Python-3.7.4`` ``fosscuda/2019b`` ========= ================== ======================================================== +.. _list_software_libGridXC_856: + +*libGridXC* ++++++++++++ + +A library to compute the exchange and correlation energy and potential in spherical (i.e. an atom) or periodic systems. It is based on SiestaXC. + +*homepage*: https://launchpad.net/libgridxc + +========= =============== +version toolchain +========= =============== +``0.8.5`` ``iimpi/2019b`` +========= =============== + + .. _list_software_libgtextutils_1428: *libgtextutils* @@ -14989,11 +15812,11 @@ libHaru is a free, cross platform, open source library for generating PDF files. *homepage*: http://libharu.org/ -========= ====================================================================================================== -version toolchain -========= ====================================================================================================== -``2.3.0`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``foss/2016a``, ``foss/2016b``, ``intel/2017a``, ``intel/2018b`` -========= ====================================================================================================== +========= ========================================================================================================================= +version toolchain +========= ========================================================================================================================= +``2.3.0`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``foss/2016a``, ``foss/2016b``, ``intel/2017a``, ``intel/2018b`` +========= ========================================================================================================================= .. _list_software_libibmad_820: @@ -15075,7 +15898,7 @@ version toolchain ======== ====================================================================================== ``1.32`` ``GCCcore/5.4.0``, ``GNU/4.9.3-2.25``, ``foss/2016a``, ``foss/2016b``, ``intel/2016a`` ``1.34`` ``GCCcore/6.4.0`` -``1.35`` ``GCCcore/7.3.0`` +``1.35`` ``GCCcore/7.3.0``, ``GCCcore/8.3.0`` ======== ====================================================================================== @@ -15203,6 +16026,7 @@ libpng is the official PNG reference library version toolchain ========== ===================================================================== ``1.2.58`` ``system`` +``1.2.59`` ``system`` ``1.6.21`` ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a`` ``1.6.23`` ``foss/2016a``, ``foss/2016b``, ``intel/2016b`` ``1.6.24`` ``GCCcore/4.9.3``, ``GCCcore/5.4.0``, ``foss/2016b``, ``intel/2016b`` @@ -15250,6 +16074,22 @@ version toolchain ========= ============================== +.. _list_software_libPSML_627: + +*libPSML* ++++++++++ + +A library to handle PSML, the pseudopotential markup language. + +*homepage*: https://launchpad.net/libpsml + +========= ======================= +version toolchain +========= ======================= +``1.1.8`` ``iccifort/2019.5.281`` +========= ======================= + + .. _list_software_libpsortb_977: *libpsortb* @@ -15529,13 +16369,13 @@ version toolchain LIBSVM is an integrated software for support vector classification, (C-SVC, nu-SVC), regression (epsilon-SVR, nu-SVR) and distribution estimation (one-class SVM). It supports multi-class classification. -*homepage*: http://www.csie.ntu.edu.tw/~cjlin/libsvm/ +*homepage*: https://www.csie.ntu.edu.tw/~cjlin/libsvm/ ======== ================================ version toolchain ======== ================================ ``3.22`` ``intel/2016b``, ``intel/2017b`` -``3.23`` ``intel/2018b`` +``3.23`` ``foss/2018b``, ``intel/2018b`` ======== ================================ @@ -15704,14 +16544,14 @@ version toolchain libvdwxc is a general library for evaluating energy and potential for exchange-correlation (XC) functionals from the vdW-DF family that can be used with various of density functional theory (DFT) codes. -*homepage*: http://libvdwxc.org +*homepage*: https://libvdwxc.org -========= ============== -version toolchain -========= ============== -``0.3.2`` ``foss/2018b`` -``0.4.0`` ``foss/2019a`` -========= ============== +========= ============================== +version toolchain +========= ============================== +``0.3.2`` ``foss/2018b`` +``0.4.0`` ``foss/2019a``, ``foss/2019b`` +========= ============================== .. _list_software_libwebp_741: @@ -15782,7 +16622,7 @@ version toolchain ``4.0.1`` ``foss/2017b``, ``intel/2017b`` ``4.0.3`` ``foss/2016b``, ``foss/2017a`` ``4.2.3`` ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``gimkl/2017a``, ``intel/2018a``, ``intel/2018b`` -``4.3.4`` ``GCC/8.2.0-2.31.1``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1`` +``4.3.4`` ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``iccifort/2019.5.281`` ========= ======================================================================================================================================= @@ -16266,6 +17106,7 @@ version toolchain ``4.1.0`` ``GCCcore/4.9.3`` ``4.2.0`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``foss/2017a``, ``intel/2017a`` ``4.3.2`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` +``5.0.1`` ``GCCcore/8.3.0`` ========= ===================================================================== @@ -16310,25 +17151,28 @@ version toolchain The LLVM Core libraries provide a modern source- and target-independent optimizer, along with code generation support for many popular CPUs (as well as some less common ones!) These libraries are built around a well specified code representation known as the LLVM intermediate representation ("LLVM IR"). The LLVM Core libraries are well documented, and it is particularly easy to invent your own language (or port an existing compiler) to use LLVM as an optimizer and code generator. -*homepage*: http://llvm.org/ +*homepage*: https://llvm.org/ -========= ======================================================================== -version toolchain -========= ======================================================================== -``3.7.1`` ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a`` -``3.8.0`` ``foss/2016a``, ``intel/2016a`` -``3.8.1`` ``GCCcore/4.9.3``, ``foss/2016b``, ``intel/2016b`` -``3.9.0`` ``foss/2016b``, ``intel/2016b`` -``3.9.1`` ``foss/2017a`` -``4.0.0`` ``foss/2017a``, ``intel/2017a`` -``4.0.1`` ``intel/2017a``, ``intel/2017b`` -``5.0.0`` ``foss/2017b``, ``fosscuda/2017b``, ``intel/2017b``, ``intelcuda/2017b`` -``5.0.1`` ``GCCcore/6.4.0`` -``6.0.0`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` -``7.0.0`` ``GCCcore/7.2.0``, ``GCCcore/7.3.0`` -``7.0.1`` ``GCCcore/8.2.0`` -``9.0.0`` ``GCCcore/8.3.0`` -========= ======================================================================== +========== ======================================================================== +version toolchain +========== ======================================================================== +``3.7.1`` ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a`` +``3.8.0`` ``foss/2016a``, ``intel/2016a`` +``3.8.1`` ``GCCcore/4.9.3``, ``foss/2016b``, ``intel/2016b`` +``3.9.0`` ``foss/2016b``, ``intel/2016b`` +``3.9.1`` ``foss/2017a`` +``4.0.0`` ``foss/2017a``, ``intel/2017a`` +``4.0.1`` ``intel/2017a``, ``intel/2017b`` +``5.0.0`` ``foss/2017b``, ``fosscuda/2017b``, ``intel/2017b``, ``intelcuda/2017b`` +``5.0.1`` ``GCCcore/6.4.0`` +``6.0.0`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` +``7.0.0`` ``GCCcore/7.2.0``, ``GCCcore/7.3.0`` +``7.0.1`` ``GCCcore/8.2.0`` +``8.0.1`` ``GCCcore/8.3.0`` +``9.0.0`` ``GCCcore/8.3.0`` +``9.0.1`` ``GCCcore/8.3.0`` +``10.0.0`` ``GCCcore/8.3.0`` +========== ======================================================================== .. _list_software_LMDB_287: @@ -16360,11 +17204,12 @@ Lmfit provides a high-level interface to non-linear optimization and curve fitti *homepage*: https://lmfit.github.io/lmfit-py -========= ================= =============== -version versionsuffix toolchain -========= ================= =============== -``0.9.9`` ``-Python-3.6.4`` ``intel/2018a`` -========= ================= =============== +========== ================== =============== +version versionsuffix toolchain +========== ================== =============== +``0.9.9`` ``-Python-3.6.4`` ``intel/2018a`` +``0.9.14`` ``-Python-2.7.15`` ``intel/2018b`` +========== ================== =============== .. _list_software_Lmod_396: @@ -16535,12 +17380,13 @@ LS-PrePost is an advanced pre and post-processor that is delivered free with LS- *homepage*: http://lstc.com/products/ls-prepost -======= ============= ========== -version versionsuffix toolchain -======= ============= ========== -``4.6`` ``-centos6`` ``system`` -``4.6`` ``-centos7`` ``system`` -======= ============= ========== +========= ============= ========== +version versionsuffix toolchain +========= ============= ========== +``4.6`` ``-centos6`` ``system`` +``4.6`` ``-centos7`` ``system`` +``4.7.8`` ``system`` +========= ============= ========== .. _list_software_LSMS_319: @@ -16559,6 +17405,22 @@ version toolchain ============ ============== +.. _list_software_LtrDetector_1132: + +*LtrDetector* ++++++++++++++ + +A modern tool-suite for detectinglong terminal repeat retrotransposons de-novo onthe genomic scale + +*homepage*: https://github.com/TulsaBioinformaticsToolsmith/LtrDetector + +======= ================= =============== +version versionsuffix toolchain +======= ================= =============== +``1.0`` ``-Python-3.7.4`` ``intel/2019b`` +======= ================= =============== + + .. _list_software_Lua_290: *Lua* @@ -16568,16 +17430,16 @@ Lua is a powerful, fast, lightweight, embeddable scripting language. Lua combin *homepage*: http://www.lua.org/ -=========== ======================================== -version toolchain -=========== ======================================== -``5.1.4-5`` ``GCC/4.8.2`` -``5.1.4-8`` ``GCC/4.8.2``, ``GCC/4.8.4``, ``system`` -``5.1.5`` ``GCCcore/7.3.0`` -``5.2.4`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` -``5.3.4`` ``GCCcore/7.2.0``, ``system`` -``5.3.5`` ``GCCcore/8.2.0``, ``system`` -=========== ======================================== +=========== ================================================ +version toolchain +=========== ================================================ +``5.1.4-5`` ``GCC/4.8.2`` +``5.1.4-8`` ``GCC/4.8.2``, ``GCC/4.8.4``, ``system`` +``5.1.5`` ``GCCcore/7.3.0``, ``GCCcore/8.3.0`` +``5.2.4`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` +``5.3.4`` ``GCCcore/7.2.0``, ``system`` +``5.3.5`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``system`` +=========== ================================================ .. _list_software_LuaJIT_521: @@ -16730,12 +17592,12 @@ Portable lossless data compression library *homepage*: http://www.oberhumer.com/opensource/lzo/ -======== ========================================================================================================================================================= -version toolchain -======== ========================================================================================================================================================= -``2.09`` ``intel/2016b``, ``intel/2017b`` -``2.10`` ``GCCcore/6.4.0``, ``GCCcore/8.2.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2017a``, ``foss/2018a``, ``foss/2018b``, ``fosscuda/2018b``, ``intel/2017a`` -======== ========================================================================================================================================================= +======== ============================================================================================================================================================================ +version toolchain +======== ============================================================================================================================================================================ +``2.09`` ``intel/2016b``, ``intel/2017b`` +``2.10`` ``GCCcore/6.4.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2017a``, ``foss/2018a``, ``foss/2018b``, ``fosscuda/2018b``, ``intel/2017a`` +======== ============================================================================================================================================================================ .. _list_software_letter_m: @@ -16744,7 +17606,7 @@ version toolchain --- -:ref:`list_software_M4_129` - :ref:`list_software_MACH_281` - :ref:`list_software_MACS2_342` - :ref:`list_software_maeparser_960` - :ref:`list_software_MAFFT_366` - :ref:`list_software_magick_620` - :ref:`list_software_magma_515` - :ref:`list_software_MAGMA_355` - :ref:`list_software_MagresPython_1249` - :ref:`list_software_mahotas_749` - :ref:`list_software_MAJIQ_370` - :ref:`list_software_make_414` - :ref:`list_software_makedepend_1038` - :ref:`list_software_makedepf90_934` - :ref:`list_software_Mako_392` - :ref:`list_software_Maple_495` - :ref:`list_software_MapSplice_894` - :ref:`list_software_Maq_287` - :ref:`list_software_MariaDB_624` - :ref:`list_software_MariaDB-connector-c_1784` - :ref:`list_software_Mash_393` - :ref:`list_software_MaSuRCA_588` - :ref:`list_software_Mathematica_1118` - :ref:`list_software_MathGL_541` - :ref:`list_software_MATIO_378` - :ref:`list_software_MATLAB_433` - :ref:`list_software_MATLAB-Engine_1076` - :ref:`list_software_matplotlib_1080` - :ref:`list_software_MATSim_523` - :ref:`list_software_Maven_503` - :ref:`list_software_mawk_432` - :ref:`list_software_MaxBin_575` - :ref:`list_software_MaxQuant_815` - :ref:`list_software_mayavi_647` - :ref:`list_software_mc_208` - :ref:`list_software_MCL_220` - :ref:`list_software_MCR_226` - :ref:`list_software_MDBM_288` - :ref:`list_software_MDSplus_680` - :ref:`list_software_mdtest_657` - :ref:`list_software_MDTraj_546` - :ref:`list_software_medaka_611` - :ref:`list_software_Meep_391` - :ref:`list_software_MEGA_282` - :ref:`list_software_MEGACC_416` - :ref:`list_software_MEGAHIT_511` - :ref:`list_software_Meld_386` - :ref:`list_software_MEME_292` - :ref:`list_software_memkind_741` - :ref:`list_software_memory-profiler_1577` - :ref:`list_software_meRanTK_658` - :ref:`list_software_MERCKX_458` - :ref:`list_software_Mercurial_932` - :ref:`list_software_Mesa_390` - :ref:`list_software_meshio_645` - :ref:`list_software_Meson_514` - :ref:`list_software_Mesquite_845` - :ref:`list_software_MetaBAT_606` - :ref:`list_software_MetaboAnalystR_1414` - :ref:`list_software_MetaGeneAnnotator_1724` - :ref:`list_software_Metal_499` - :ref:`list_software_MetaPhlAn2_908` - :ref:`list_software_metaWRAP_737` - :ref:`list_software_Metaxa2_658` - :ref:`list_software_MethylDackel_1207` - :ref:`list_software_methylpy_892` - :ref:`list_software_METIS_386` - :ref:`list_software_mhcflurry_988` - :ref:`list_software_MiGEC_389` - :ref:`list_software_MIGRATE-N_644` - :ref:`list_software_MINC_295` - :ref:`list_software_Miniconda2_964` - :ref:`list_software_Miniconda3_965` - :ref:`list_software_minieigen_949` - :ref:`list_software_Minimac4_754` - :ref:`list_software_minimap2_797` - :ref:`list_software_MinPath_689` - :ref:`list_software_MIRA_297` - :ref:`list_software_miRDeep2_728` - :ref:`list_software_MiXCR_419` - :ref:`list_software_mkl-dnn_689` - :ref:`list_software_mkl-service_1122` - :ref:`list_software_MLC_220` - :ref:`list_software_Mmg_289` - :ref:`list_software_MMSEQ_387` - :ref:`list_software_MMseqs2_648` - :ref:`list_software_modred_635` - :ref:`list_software_Molcas_607` - :ref:`list_software_Molden_607` - :ref:`list_software_Molekel_713` - :ref:`list_software_molmod_648` - :ref:`list_software_Molpro_633` - :ref:`list_software_Mono_409` - :ref:`list_software_mordecai_836` - :ref:`list_software_mosdepth_868` - :ref:`list_software_Mothur_639` - :ref:`list_software_motif_543` - :ref:`list_software_MotionCor2_972` - :ref:`list_software_MoviePy_713` - :ref:`list_software_MPC_224` - :ref:`list_software_MPFR_309` - :ref:`list_software_mpi4py_611` - :ref:`list_software_MPICH_369` - :ref:`list_software_MPICH2_419` - :ref:`list_software_mpifileutils_1303` - :ref:`list_software_mpiP_406` - :ref:`list_software_MPJ-Express_1022` - :ref:`list_software_mpmath_647` - :ref:`list_software_MrBayes_691` - :ref:`list_software_MRIcron_666` - :ref:`list_software_MRtrix_614` - :ref:`list_software_MSM_237` - :ref:`list_software_MSPC_307` - :ref:`list_software_msprime_765` - :ref:`list_software_MTL4_289` - :ref:`list_software_MultiNest_933` - :ref:`list_software_MultiQC_671` - :ref:`list_software_Multiwfn_854` - :ref:`list_software_MUMmer_563` - :ref:`list_software_MUMPS_402` - :ref:`list_software_muParser_847` - :ref:`list_software_MuPeXI_536` - :ref:`list_software_MUSCLE_457` - :ref:`list_software_MuSiC_449` - :ref:`list_software_MuTect_594` - :ref:`list_software_mutil_555` - :ref:`list_software_MVAPICH2_570` - :ref:`list_software_MXNet_460` - :ref:`list_software_mygene_645` - :ref:`list_software_MyMediaLite_1076` - :ref:`list_software_mympingpong_1205` - :ref:`list_software_mypy_463` - :ref:`list_software_MySQL_438` - :ref:`list_software_MySQL-python_1157` - :ref:`list_software_mysqlclient_1205` +:ref:`list_software_M4_129` - :ref:`list_software_MACH_281` - :ref:`list_software_MACS2_342` - :ref:`list_software_maeparser_960` - :ref:`list_software_MAFFT_366` - :ref:`list_software_magick_620` - :ref:`list_software_magma_515` - :ref:`list_software_MAGMA_355` - :ref:`list_software_MagresPython_1249` - :ref:`list_software_mahotas_749` - :ref:`list_software_MAJIQ_370` - :ref:`list_software_make_414` - :ref:`list_software_makedepend_1038` - :ref:`list_software_makedepf90_934` - :ref:`list_software_Mako_392` - :ref:`list_software_manta_529` - :ref:`list_software_Maple_495` - :ref:`list_software_MapSplice_894` - :ref:`list_software_Maq_287` - :ref:`list_software_MariaDB_624` - :ref:`list_software_MariaDB-connector-c_1784` - :ref:`list_software_Mash_393` - :ref:`list_software_MaSuRCA_588` - :ref:`list_software_Mathematica_1118` - :ref:`list_software_MathGL_541` - :ref:`list_software_MATIO_378` - :ref:`list_software_MATLAB_433` - :ref:`list_software_MATLAB-Engine_1076` - :ref:`list_software_matplotlib_1080` - :ref:`list_software_MATSim_523` - :ref:`list_software_Maven_503` - :ref:`list_software_mawk_432` - :ref:`list_software_MaxBin_575` - :ref:`list_software_MaxQuant_815` - :ref:`list_software_mayavi_647` - :ref:`list_software_mc_208` - :ref:`list_software_MCL_220` - :ref:`list_software_MCR_226` - :ref:`list_software_MDBM_288` - :ref:`list_software_MDSplus_680` - :ref:`list_software_mdtest_657` - :ref:`list_software_MDTraj_546` - :ref:`list_software_medaka_611` - :ref:`list_software_medImgProc_999` - :ref:`list_software_MedPy_479` - :ref:`list_software_Meep_391` - :ref:`list_software_MEGA_282` - :ref:`list_software_MEGACC_416` - :ref:`list_software_MEGAHIT_511` - :ref:`list_software_Meld_386` - :ref:`list_software_MEME_292` - :ref:`list_software_memkind_741` - :ref:`list_software_memory-profiler_1577` - :ref:`list_software_meRanTK_658` - :ref:`list_software_MERCKX_458` - :ref:`list_software_Mercurial_932` - :ref:`list_software_Mesa_390` - :ref:`list_software_meshio_645` - :ref:`list_software_Meson_514` - :ref:`list_software_Mesquite_845` - :ref:`list_software_MetaBAT_606` - :ref:`list_software_MetaboAnalystR_1414` - :ref:`list_software_MetaGeneAnnotator_1724` - :ref:`list_software_Metal_499` - :ref:`list_software_MetaPhlAn2_908` - :ref:`list_software_metaWRAP_737` - :ref:`list_software_Metaxa2_658` - :ref:`list_software_MethylDackel_1207` - :ref:`list_software_methylpy_892` - :ref:`list_software_METIS_386` - :ref:`list_software_mhcflurry_988` - :ref:`list_software_MiGEC_389` - :ref:`list_software_MIGRATE-N_644` - :ref:`list_software_MINC_295` - :ref:`list_software_Mini-XML_683` - :ref:`list_software_Miniconda2_964` - :ref:`list_software_Miniconda3_965` - :ref:`list_software_minieigen_949` - :ref:`list_software_Minimac4_754` - :ref:`list_software_minimap2_797` - :ref:`list_software_MinPath_689` - :ref:`list_software_MIRA_297` - :ref:`list_software_miRDeep2_728` - :ref:`list_software_MiXCR_419` - :ref:`list_software_mkl-dnn_689` - :ref:`list_software_mkl-service_1122` - :ref:`list_software_mkl_fft_739` - :ref:`list_software_MLC_220` - :ref:`list_software_Mmg_289` - :ref:`list_software_MMSEQ_387` - :ref:`list_software_MMseqs2_648` - :ref:`list_software_modred_635` - :ref:`list_software_Molcas_607` - :ref:`list_software_Molden_607` - :ref:`list_software_Molekel_713` - :ref:`list_software_molmod_648` - :ref:`list_software_Molpro_633` - :ref:`list_software_Mono_409` - :ref:`list_software_Monocle3_768` - :ref:`list_software_mordecai_836` - :ref:`list_software_MoreRONN_720` - :ref:`list_software_mosdepth_868` - :ref:`list_software_Mothur_639` - :ref:`list_software_motif_543` - :ref:`list_software_MotionCor2_972` - :ref:`list_software_motionSegmentation_1924` - :ref:`list_software_MoviePy_713` - :ref:`list_software_MPC_224` - :ref:`list_software_MPFR_309` - :ref:`list_software_mpi4py_611` - :ref:`list_software_MPICH_369` - :ref:`list_software_MPICH2_419` - :ref:`list_software_mpifileutils_1303` - :ref:`list_software_mpiP_406` - :ref:`list_software_MPJ-Express_1022` - :ref:`list_software_mpmath_647` - :ref:`list_software_MrBayes_691` - :ref:`list_software_MRIcron_666` - :ref:`list_software_MRtrix_614` - :ref:`list_software_MSM_237` - :ref:`list_software_MSPC_307` - :ref:`list_software_msprime_765` - :ref:`list_software_MTL4_289` - :ref:`list_software_MultiNest_933` - :ref:`list_software_MultiQC_671` - :ref:`list_software_Multiwfn_854` - :ref:`list_software_MUMmer_563` - :ref:`list_software_MUMPS_402` - :ref:`list_software_muParser_847` - :ref:`list_software_MuPeXI_536` - :ref:`list_software_MUSCLE_457` - :ref:`list_software_MuSiC_449` - :ref:`list_software_MuTect_594` - :ref:`list_software_mutil_555` - :ref:`list_software_MVAPICH2_570` - :ref:`list_software_MXNet_460` - :ref:`list_software_mygene_645` - :ref:`list_software_MyMediaLite_1076` - :ref:`list_software_mympingpong_1205` - :ref:`list_software_mypy_463` - :ref:`list_software_MySQL_438` - :ref:`list_software_MySQL-python_1157` - :ref:`list_software_mysqlclient_1205` .. _list_software_M4_129: @@ -16761,7 +17623,7 @@ version toolchain ========== =========================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== ``1.4.16`` ``GCC/4.8.1``, ``GCC/4.8.2``, ``system`` ``1.4.17`` ``GCC/4.8.2``, ``GCC/4.8.4``, ``GCC/4.9.2``, ``GCC/4.9.2-binutils-2.25``, ``GCC/4.9.3``, ``GCC/4.9.3-2.25``, ``GCC/4.9.3-binutils-2.25``, ``GCC/5.1.0-binutils-2.25``, ``GCC/5.2.0``, ``GCC/5.4.0-2.26``, ``GCCcore/4.9.2``, ``GCCcore/4.9.3``, ``GCCcore/4.9.4``, ``GCCcore/5.3.0``, ``GCCcore/5.4.0``, ``GCCcore/6.1.0``, ``GCCcore/6.2.0``, ``GNU/4.9.2-2.25``, ``GNU/4.9.3-2.25``, ``GNU/5.1.0-2.25``, ``foss/2016.04``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``intel/2016.02-GCC-4.9``, ``intel/2016a``, ``intel/2016b``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25``, ``system`` -``1.4.18`` ``GCCcore/5.3.0``, ``GCCcore/5.4.0``, ``GCCcore/5.5.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.1.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/7.4.0``, ``GCCcore/8.1.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.1.0``, ``GCCcore/9.2.0``, ``GCCcore/system``, ``system`` +``1.4.18`` ``GCCcore/5.3.0``, ``GCCcore/5.4.0``, ``GCCcore/5.5.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.1.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/7.4.0``, ``GCCcore/8.1.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.1.0``, ``GCCcore/9.2.0``, ``GCCcore/9.3.0``, ``GCCcore/system``, ``system`` ========== =========================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== @@ -16825,14 +17687,15 @@ MAFFT is a multiple sequence alignment program for unix-like operating systems *homepage*: https://mafft.cbrc.jp/alignment/software/source.html -========= ==================== ==================== -version versionsuffix toolchain -========= ==================== ==================== -``7.305`` ``-with-extensions`` ``foss/2016b`` -``7.397`` ``-with-extensions`` ``intel/2018a`` -``7.427`` ``-with-extensions`` ``intel/2018b`` -``7.429`` ``-with-extensions`` ``GCC/8.2.0-2.31.1`` -========= ==================== ==================== +========= ==================== ====================================== +version versionsuffix toolchain +========= ==================== ====================================== +``7.305`` ``-with-extensions`` ``foss/2016b`` +``7.397`` ``-with-extensions`` ``intel/2018a`` +``7.427`` ``-with-extensions`` ``intel/2018b`` +``7.429`` ``-with-extensions`` ``GCC/8.2.0-2.31.1`` +``7.453`` ``-with-extensions`` ``GCC/8.3.0``, ``iccifort/2019.5.281`` +========= ==================== ====================================== .. _list_software_magick_620: @@ -17009,6 +17872,23 @@ version versionsuffix toolchain ========= ================== ================================================================================================================================================================= +.. _list_software_manta_529: + +*manta* ++++++++ + +Manta calls structural variants (SVs) and indels from mapped paired-end sequencing reads. It is optimized for analysis of germline variation in small sets of individuals and somatic variation in tumor/normal sample pairs. Manta discovers, assembles and scores large-scale SVs, medium-sized indels and large insertions within a single efficient workflow. + +*homepage*: https://github.com/Illumina/manta + +========= ========== +version toolchain +========= ========== +``1.1.1`` ``system`` +``1.6.0`` ``system`` +========= ========== + + .. _list_software_Maple_495: *Maple* @@ -17092,13 +17972,13 @@ MariaDB Connector/C is used to connect applications developed in C/C++ to MariaD *homepage*: https://downloads.mariadb.org/connector-c/ -========= ================================= -version toolchain -========= ================================= -``2.3.4`` ``foss/2017b``, ``intel/2017b`` -``2.3.5`` ``intel/2018a``, ``iomkl/2018a`` -``2.3.7`` ``GCCcore/8.2.0``, ``foss/2018b`` -========= ================================= +========= ==================================================== +version toolchain +========= ==================================================== +``2.3.4`` ``foss/2017b``, ``intel/2017b`` +``2.3.5`` ``intel/2018a``, ``iomkl/2018a`` +``2.3.7`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``foss/2018b`` +========= ==================================================== .. _list_software_Mash_393: @@ -17202,7 +18082,7 @@ version toolchain MATLAB is a high-level language and interactive environment that enables you to perform computationally intensive tasks faster than with traditional programming languages such as C, C++, and Fortran. -*homepage*: http://www.mathworks.com/products/matlab +*homepage*: https://www.mathworks.com/products/matlab.html ========= ========== version toolchain @@ -17213,6 +18093,7 @@ version toolchain ``2016a`` ``system`` ``2017a`` ``system`` ``2018b`` ``system`` +``2019b`` ``system`` ========= ========== @@ -17273,10 +18154,12 @@ version versionsuffix toolchain ``2.2.3`` ``-Python-2.7.15`` ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b`` ``2.2.3`` ``-Python-3.6.6`` ``intel/2018b`` ``2.2.4`` ``-Python-2.7.15`` ``foss/2019a``, ``fosscuda/2019a``, ``intel/2019a``, ``intelcuda/2019a`` +``2.2.4`` ``-Python-2.7.16`` ``foss/2019b``, ``intel/2019b`` +``2.2.5`` ``-Python-2.7.16`` ``foss/2019b`` ``3.0.0`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b``, ``iomkl/2018b`` ``3.0.2`` ``-Python-3.6.6`` ``foss/2018b`` ``3.0.3`` ``-Python-3.7.2`` ``foss/2019a``, ``fosscuda/2019a``, ``intel/2019a``, ``intelcuda/2019a`` -``3.1.1`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` +``3.1.1`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b`` ========= ================================= ======================================================================== @@ -17314,6 +18197,7 @@ version toolchain ``3.5.0`` ``system`` ``3.5.2`` ``system`` ``3.6.0`` ``system`` +``3.6.3`` ``system`` ========= ========== @@ -17380,6 +18264,7 @@ The Mayavi scientific data 3-dimensional visualizer version versionsuffix toolchain ========= ================== =============== ``4.4.4`` ``-Python-2.7.11`` ``intel/2016a`` +``4.7.1`` ``-Python-2.7.15`` ``foss/2019a`` ``4.7.1`` ``-Python-3.7.2`` ``foss/2019a`` ========= ================== =============== @@ -17409,14 +18294,14 @@ The MCL algorithm is short for the Markov Cluster Algorithm, a fast and scalable *homepage*: http://micans.org/mcl/ -========== ================ =============================== -version versionsuffix toolchain -========== ================ =============================== -``02.063`` ``intel/2016b`` -``14.137`` ``foss/2016a``, ``intel/2016b`` -``14.137`` ``-Perl-5.26.1`` ``GCCcore/6.4.0`` -``14.137`` ``-Perl-5.28.0`` ``GCCcore/7.3.0`` -========== ================ =============================== +========== ================ ================================================== +version versionsuffix toolchain +========== ================ ================================================== +``02.063`` ``intel/2016b`` +``14.137`` ``GCCcore/8.3.0``, ``foss/2016a``, ``intel/2016b`` +``14.137`` ``-Perl-5.26.1`` ``GCCcore/6.4.0`` +``14.137`` ``-Perl-5.28.0`` ``GCCcore/7.3.0`` +========== ================ ================================================== .. _list_software_MCR_226: @@ -17521,17 +18406,51 @@ medaka is a tool to create a consensus sequence of nanopore sequencing data. *homepage*: https://nanoporetech.github.io/medaka +========== ================= ============== +version versionsuffix toolchain +========== ================= ============== +``0.4.3`` ``-Python-3.6.6`` ``foss/2018b`` +``0.11.4`` ``-Python-3.6.6`` ``foss/2018b`` +``0.12.0`` ``-Python-3.6.6`` ``foss/2018b`` +========== ================= ============== + + +.. _list_software_medImgProc_999: + +*medImgProc* +++++++++++++ + +Motion correction, explicit spatio-temporal regularization of motion tracking, random speckles enhancement, and segmentation. + +*homepage*: https://github.com/WeiXuanChan/motionSegmentation + ========= ================= ============== version versionsuffix toolchain ========= ================= ============== -``0.4.3`` ``-Python-3.6.6`` ``foss/2018b`` +``2.5.7`` ``-Python-3.7.4`` ``foss/2019b`` ========= ================= ============== -.. _list_software_Meep_391: +.. _list_software_MedPy_479: -*Meep* -++++++ +*MedPy* ++++++++ + +MedPy is a library and script collection for medical image processing in Python, providing basic functionalities for reading, writing and manipulating large images of arbitrary dimensionality. Its main contributions are n-dimensional versions of popular image filters, a collection of image feature extractors, ready to be used with scikit-learn, and an exhaustive n-dimensional graph-cut package. + +*homepage*: https://pypi.org/project/MedPy/ + +========= ================= ============== +version versionsuffix toolchain +========= ================= ============== +``0.4.0`` ``-Python-3.7.4`` ``foss/2019b`` +========= ================= ============== + + +.. _list_software_Meep_391: + +*Meep* +++++++ Meep (or MEEP) is a free finite-difference time-domain (FDTD) simulation software package developed at MIT to model electromagnetic systems. @@ -17772,6 +18691,7 @@ version versionsuffix toolchain ``0.48.1`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b`` ``0.50.0`` ``-Python-3.7.2`` ``GCCcore/8.2.0`` ``0.51.2`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` +``0.53.1`` ``-Python-3.6.3`` ``intel/2017b`` ========== ================= ================================== @@ -17919,6 +18839,7 @@ A (mostly) universal methylation extractor for BS-seq experiments. version toolchain ========= ======================================== ``0.4.0`` ``iccifort/2019.1.144-GCC-8.2.0-2.31.1`` +``0.5.0`` ``iccifort/2019.5.281`` ========= ======================================== @@ -18021,6 +18942,22 @@ version toolchain ========== =============================================== +.. _list_software_Mini-XML_683: + +*Mini-XML* +++++++++++ + +Mini-XML is a tiny XML library that you can use to read and write XML and XML-like data files in your application without requiring large non-standard libraries. + +*homepage*: https://www.msweet.org/mxml/ + +======= ================= +version toolchain +======= ================= +``2.9`` ``GCCcore/8.2.0`` +======= ================= + + .. _list_software_Miniconda2_964: *Miniconda2* @@ -18217,6 +19154,22 @@ version toolchain ========= =============== +.. _list_software_mkl_fft_739: + +*mkl_fft* ++++++++++ + +NumPy-based Python interface to Intel(R) MKL FFT functionality + +*homepage*: https://github.com/IntelPython/mkl_fft + +========== ================= =============== +version versionsuffix toolchain +========== ================= =============== +``1.0.14`` ``-Python-3.6.6`` ``intel/2018b`` +========== ================= =============== + + .. _list_software_MLC_220: *MLC* @@ -18274,13 +19227,14 @@ MMseqs2: ultra fast and sensitive search and clustering suite *homepage*: https://mmseqs.com -=========== =============== -version toolchain -=========== =============== -``1-c7a89`` ``foss/2016b`` -``5-9375b`` ``intel/2018a`` -``8-fac81`` ``intel/2018b`` -=========== =============== +============ ================================ +version toolchain +============ ================================ +``1-c7a89`` ``foss/2016b`` +``5-9375b`` ``intel/2018a`` +``8-fac81`` ``intel/2018b`` +``10-6d92c`` ``gompi/2019b``, ``iimpi/2019b`` +============ ================================ .. _list_software_modred_635: @@ -18372,7 +19326,7 @@ version versionsuffix toolchain ``1.4.4`` ``-Python-2.7.14`` ``foss/2018a``, ``intel/2018a`` ``1.4.4`` ``-Python-2.7.15`` ``intel/2018b`` ``1.4.4`` ``-Python-3.7.2`` ``intel/2019a`` -``1.4.5`` ``-Python-3.7.4`` ``intel/2019b`` +``1.4.5`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` ========= ================== =============================== @@ -18414,9 +19368,26 @@ version toolchain ``5.10.0.160`` ``foss/2018a`` ``5.18.1.0`` ``foss/2018a`` ``6.4.0.198`` ``foss/2018b`` +``6.8.0.105`` ``GCCcore/8.3.0`` ============== =============================== +.. _list_software_Monocle3_768: + +*Monocle3* +++++++++++ + +An analysis toolkit for single-cell RNA-seq. + +*homepage*: https://cole-trapnell-lab.github.io/monocle3/ + +========= ========================= ============== +version versionsuffix toolchain +========= ========================= ============== +``0.2.0`` ``-Python-3.7.2-R-3.6.0`` ``foss/2019a`` +========= ========================= ============== + + .. _list_software_mordecai_836: *mordecai* @@ -18433,6 +19404,22 @@ version versionsuffix toolchain ========= ================= ============== +.. _list_software_MoreRONN_720: + +*MoreRONN* +++++++++++ + +MoreRONN is the spiritual successor of RONN and is useful for surveying disorder in proteins as well as designing expressible constructs for X-ray crystallography. + +*homepage*: https://github.com/varun-ramraj/MoreRONN + +======= ============= +version toolchain +======= ============= +``4.9`` ``GCC/8.3.0`` +======= ============= + + .. _list_software_mosdepth_868: *mosdepth* @@ -18476,15 +19463,15 @@ version versionsuffix toolchain Motif refers to both a graphical user interface (GUI) specification and the widget toolkit for building applications that follow that specification under the X Window System on Unix and other POSIX-compliant systems. It was the standard toolkit for the Common Desktop Environment and thus for Unix. -*homepage*: http://motif.ics.com/ +*homepage*: https://motif.ics.com/ -========= ================================================================================ -version toolchain -========= ================================================================================ -``2.3.5`` ``foss/2016a``, ``intel/2016a`` -``2.3.7`` ``intel/2017a`` -``2.3.8`` ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``intel/2017b``, ``intel/2018a`` -========= ================================================================================ +========= ==================================================================================================================================== +version toolchain +========= ==================================================================================================================================== +``2.3.5`` ``foss/2016a``, ``intel/2016a`` +``2.3.7`` ``intel/2017a`` +``2.3.8`` ``GCCcore/8.3.0``, ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``foss/2019a``, ``intel/2017b``, ``intel/2018a``, ``intel/2019a`` +========= ==================================================================================================================================== .. _list_software_MotionCor2_972: @@ -18503,6 +19490,22 @@ version toolchain ========= ================= +.. _list_software_motionSegmentation_1924: + +*motionSegmentation* +++++++++++++++++++++ + +Motion correction, explicit spatio-temporal regularization of motion tracking, random speckles enhancement, and segmentation. + +*homepage*: https://github.com/WeiXuanChan/motionSegmentation + +========= ================= ============== +version versionsuffix toolchain +========= ================= ============== +``2.7.9`` ``-Python-3.7.4`` ``foss/2019b`` +========= ================= ============== + + .. _list_software_MoviePy_713: *MoviePy* @@ -18880,13 +19883,13 @@ A parallel sparse direct solver *homepage*: http://graal.ens-lyon.fr/MUMPS/ -========= ============== =============================== -version versionsuffix toolchain -========= ============== =============================== -``5.1.2`` ``-metis`` ``foss/2017b`` -``5.2.1`` ``-metis`` ``foss/2019a``, ``intel/2019a`` -``5.2.1`` ``-metis-seq`` ``foss/2019a``, ``intel/2019a`` -========= ============== =============================== +========= ============== ================================================================================ +version versionsuffix toolchain +========= ============== ================================================================================ +``5.1.2`` ``-metis`` ``foss/2017b`` +``5.2.1`` ``-metis`` ``foss/2018b``, ``foss/2019a``, ``foss/2019b``, ``intel/2019a``, ``intel/2019b`` +``5.2.1`` ``-metis-seq`` ``foss/2019a``, ``intel/2019a`` +========= ============== ================================================================================ .. _list_software_muParser_847: @@ -18935,7 +19938,7 @@ version versionsuffix toolchain ============ =============== ================================================================================================================== ``3.8.31`` ``foss/2016a``, ``foss/2017b``, ``foss/2018a``, ``intel/2016a``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b`` ``3.8.31`` ``-i86linux64`` ``system`` -``3.8.1551`` ``GCC/8.2.0-2.31.1`` +``3.8.1551`` ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0`` ============ =============== ================================================================================================================== @@ -19149,7 +20152,7 @@ version versionsuffix toolchain --- -:ref:`list_software_NAG_214` - :ref:`list_software_NAGfor_541` - :ref:`list_software_NAMD_288` - :ref:`list_software_nanofilt_859` - :ref:`list_software_nanonet_755` - :ref:`list_software_nanopolish_1083` - :ref:`list_software_NASM_303` - :ref:`list_software_NBO_223` - :ref:`list_software_NCBI-Toolkit_1071` - :ref:`list_software_ncbi-vdb_773` - :ref:`list_software_NCCL_288` - :ref:`list_software_ncdf4_463` - :ref:`list_software_ncdu_426` - :ref:`list_software_NCIPLOT_537` - :ref:`list_software_NCL_221` - :ref:`list_software_ncl_317` - :ref:`list_software_NCO_224` - :ref:`list_software_ncompress_986` - :ref:`list_software_ncurses_771` - :ref:`list_software_ncview_652` - :ref:`list_software_nd2reader_887` - :ref:`list_software_ne_211` - :ref:`list_software_NEdit_468` - :ref:`list_software_Net-core_765` - :ref:`list_software_netCDF_532` - :ref:`list_software_netCDF-C++_730` - :ref:`list_software_netCDF-C++4_782` - :ref:`list_software_netCDF-Fortran_1309` - :ref:`list_software_netcdf4-python_1399` - :ref:`list_software_netloc_645` - :ref:`list_software_NetLogo_696` - :ref:`list_software_netMHC_543` - :ref:`list_software_netMHCIIpan_1008` - :ref:`list_software_netMHCpan_862` - :ref:`list_software_NetPIPE_597` - :ref:`list_software_nettle_652` - :ref:`list_software_networkx_898` - :ref:`list_software_NeuroKit_817` - :ref:`list_software_NEURON_471` - :ref:`list_software_Nextflow_855` - :ref:`list_software_NextGenMap_983` - :ref:`list_software_NFFT_302` - :ref:`list_software_nglview_764` - :ref:`list_software_NGS_232` - :ref:`list_software_NGS-Python_919` - :ref:`list_software_NGSadmix_763` - :ref:`list_software_NiBabel_653` - :ref:`list_software_NIfTI_410` - :ref:`list_software_Nilearn_713` - :ref:`list_software_Nim_292` - :ref:`list_software_NIMBLE_439` - :ref:`list_software_Ninja_496` - :ref:`list_software_Nipype_629` - :ref:`list_software_NLopt_493` - :ref:`list_software_NLTK_313` - :ref:`list_software_Node-RED_654` - :ref:`list_software_nodejs_643` - :ref:`list_software_Normaliz_844` - :ref:`list_software_nose-parameterized_1871` - :ref:`list_software_novoalign_973` - :ref:`list_software_NOVOPlasty_959` - :ref:`list_software_npstat_666` - :ref:`list_software_NRGLjubljana_1146` - :ref:`list_software_NSPR_323` - :ref:`list_software_NSS_244` - :ref:`list_software_numactl_756` - :ref:`list_software_numba_531` - :ref:`list_software_numexpr_783` - :ref:`list_software_numpy_569` - :ref:`list_software_nvtop_567` - :ref:`list_software_NWChem_546` - :ref:`list_software_NxTrim_610` +:ref:`list_software_NAG_214` - :ref:`list_software_NAGfor_541` - :ref:`list_software_NAMD_288` - :ref:`list_software_NanoComp_795` - :ref:`list_software_nanofilt_859` - :ref:`list_software_NanoFilt_795` - :ref:`list_software_nanoget_748` - :ref:`list_software_nanomath_854` - :ref:`list_software_nanonet_755` - :ref:`list_software_NanoPlot_811` - :ref:`list_software_nanopolish_1083` - :ref:`list_software_NASM_303` - :ref:`list_software_NBO_223` - :ref:`list_software_NCBI-Toolkit_1071` - :ref:`list_software_ncbi-vdb_773` - :ref:`list_software_NCCL_288` - :ref:`list_software_ncdf4_463` - :ref:`list_software_ncdu_426` - :ref:`list_software_NCIPLOT_537` - :ref:`list_software_NCL_221` - :ref:`list_software_ncl_317` - :ref:`list_software_NCO_224` - :ref:`list_software_ncompress_986` - :ref:`list_software_ncurses_771` - :ref:`list_software_ncview_652` - :ref:`list_software_nd2reader_887` - :ref:`list_software_ne_211` - :ref:`list_software_NEdit_468` - :ref:`list_software_Net-core_765` - :ref:`list_software_netCDF_532` - :ref:`list_software_netCDF-C++_730` - :ref:`list_software_netCDF-C++4_782` - :ref:`list_software_netCDF-Fortran_1309` - :ref:`list_software_netcdf4-python_1399` - :ref:`list_software_netloc_645` - :ref:`list_software_NetLogo_696` - :ref:`list_software_netMHC_543` - :ref:`list_software_netMHCIIpan_1008` - :ref:`list_software_netMHCpan_862` - :ref:`list_software_NetPIPE_597` - :ref:`list_software_nettle_652` - :ref:`list_software_networkx_898` - :ref:`list_software_NeuroKit_817` - :ref:`list_software_NEURON_471` - :ref:`list_software_Nextflow_855` - :ref:`list_software_NextGenMap_983` - :ref:`list_software_NFFT_302` - :ref:`list_software_nglview_764` - :ref:`list_software_NGS_232` - :ref:`list_software_NGS-Python_919` - :ref:`list_software_NGSadmix_763` - :ref:`list_software_ngspice_745` - :ref:`list_software_NiBabel_653` - :ref:`list_software_NIfTI_410` - :ref:`list_software_Nilearn_713` - :ref:`list_software_Nim_292` - :ref:`list_software_NIMBLE_439` - :ref:`list_software_Ninja_496` - :ref:`list_software_Nipype_629` - :ref:`list_software_NLopt_493` - :ref:`list_software_NLTK_313` - :ref:`list_software_Node-RED_654` - :ref:`list_software_nodejs_643` - :ref:`list_software_Normaliz_844` - :ref:`list_software_nose-parameterized_1871` - :ref:`list_software_novoalign_973` - :ref:`list_software_NOVOPlasty_959` - :ref:`list_software_npstat_666` - :ref:`list_software_NRGLjubljana_1146` - :ref:`list_software_NSPR_323` - :ref:`list_software_NSS_244` - :ref:`list_software_ntEdit_616` - :ref:`list_software_ntHits_634` - :ref:`list_software_numactl_756` - :ref:`list_software_numba_531` - :ref:`list_software_numexpr_783` - :ref:`list_software_numpy_569` - :ref:`list_software_nvtop_567` - :ref:`list_software_NWChem_546` - :ref:`list_software_NxTrim_610` .. _list_software_NAG_214: @@ -19204,6 +20207,22 @@ version versionsuffix toolchain ======== ============= ================================================================ +.. _list_software_NanoComp_795: + +*NanoComp* +++++++++++ + +Comparing runs of Oxford Nanopore sequencing data and alignments + +*homepage*: https://github.com/wdecoster/NanoComp + +========== ================= =============== +version versionsuffix toolchain +========== ================= =============== +``1.10.1`` ``-Python-3.7.4`` ``intel/2019b`` +========== ================= =============== + + .. _list_software_nanofilt_859: *nanofilt* @@ -19220,6 +20239,54 @@ version versionsuffix toolchain ========= ================= ============== +.. _list_software_NanoFilt_795: + +*NanoFilt* +++++++++++ + +Filtering and trimming of Oxford Nanopore Sequencing data + +*homepage*: https://github.com/wdecoster/nanofilt + +========= ================= =============== +version versionsuffix toolchain +========= ================= =============== +``2.6.0`` ``-Python-3.7.4`` ``intel/2019b`` +========= ================= =============== + + +.. _list_software_nanoget_748: + +*nanoget* ++++++++++ + +Functions to extract information from Oxford Nanopore sequencing data and alignments + +*homepage*: https://github.com/wdecoster/nanoget + +========== ================= =============== +version versionsuffix toolchain +========== ================= =============== +``1.12.1`` ``-Python-3.7.4`` ``intel/2019b`` +========== ================= =============== + + +.. _list_software_nanomath_854: + +*nanomath* +++++++++++ + +A few simple math function for other Oxford Nanopore processing scripts + +*homepage*: https://github.com/wdecoster/nanomath + +========== ================= =============== +version versionsuffix toolchain +========== ================= =============== +``0.23.1`` ``-Python-3.7.4`` ``intel/2019b`` +========== ================= =============== + + .. _list_software_nanonet_755: *nanonet* @@ -19236,6 +20303,22 @@ version versionsuffix toolchain ========= ================== =============== +.. _list_software_NanoPlot_811: + +*NanoPlot* +++++++++++ + +Plotting suite for long read sequencing data and alignments + +*homepage*: https://github.com/wdecoster/NanoPlot + +========== ================= =============== +version versionsuffix toolchain +========== ================= =============== +``1.28.4`` ``-Python-3.7.4`` ``intel/2019b`` +========== ================= =============== + + .. _list_software_nanopolish_1083: *nanopolish* @@ -19364,6 +20447,7 @@ version versionsuffix toolchain ``1.16`` ``-R-3.4.4`` ``intel/2018a`` ``1.16.1`` ``-R-3.5.1`` ``foss/2018b``, ``intel/2018b`` ``1.16.1`` ``-R-3.6.0`` ``foss/2019a`` +``1.17`` ``foss/2019b`` ========== ============= =============================== @@ -19480,7 +20564,7 @@ version toolchain The Ncurses (new curses) library is a free software emulation of curses in System V Release 4.0, and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses. -*homepage*: http://www.gnu.org/software/ncurses/ +*homepage*: https://www.gnu.org/software/ncurses/ ======= ============================================================================================================================================================================================================================================================================================================================================================================= version toolchain @@ -19654,7 +20738,7 @@ version versionsuffix toolchain ``4.4.4`` ``-HDF5-1.8.18`` ``intel/2017a`` ``4.4.4`` ``-HDF5-1.8.19`` ``foss/2017b``, ``intel/2017b`` ``4.4.5`` ``gompi/2019a``, ``iimpi/2019a`` -``4.5.2`` ``iimpi/2019b`` +``4.5.2`` ``gompi/2019b``, ``iimpi/2019b`` ========= ================ ==================================================================================================================================================================================================================================================================================================================================== @@ -19680,6 +20764,7 @@ version versionsuffix toolchain ``1.4.2`` ``-Python-3.6.4`` ``foss/2018a`` ``1.4.3`` ``-Python-3.6.6`` ``foss/2018b`` ``1.5.2`` ``intel/2019a`` +``1.5.3`` ``-Python-3.7.4`` ``intel/2019b`` ========= ============================= =============== @@ -19810,21 +20895,21 @@ NetworkX is a Python package for the creation, manipulation, and study of the st *homepage*: https://pypi.python.org/pypi/networkx -======== ================== =============================== -version versionsuffix toolchain -======== ================== =============================== -``1.1`` ``-Python-2.7.12`` ``intel/2016b`` -``1.11`` ``-Python-2.7.11`` ``foss/2016a`` -``1.11`` ``-Python-2.7.14`` ``intel/2017b`` -``1.11`` ``-Python-3.5.1`` ``foss/2016a`` -``2.0`` ``-Python-2.7.14`` ``intel/2017b`` -``2.1`` ``-Python-2.7.14`` ``intel/2017b`` -``2.2`` ``-Python-2.7.15`` ``intel/2018b`` -``2.2`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` -``2.3`` ``-Python-3.7.2`` ``foss/2019a``, ``intel/2019a`` -``2.4`` ``-Python-3.7.2`` ``foss/2019a``, ``intel/2019a`` -``2.4`` ``-Python-3.7.4`` ``foss/2019b`` -======== ================== =============================== +======== ================== =============================================== +version versionsuffix toolchain +======== ================== =============================================== +``1.1`` ``-Python-2.7.12`` ``intel/2016b`` +``1.11`` ``-Python-2.7.11`` ``foss/2016a`` +``1.11`` ``-Python-2.7.14`` ``intel/2017b`` +``1.11`` ``-Python-3.5.1`` ``foss/2016a`` +``2.0`` ``-Python-2.7.14`` ``intel/2017b`` +``2.1`` ``-Python-2.7.14`` ``intel/2017b`` +``2.2`` ``-Python-2.7.15`` ``foss/2018b``, ``foss/2019a``, ``intel/2018b`` +``2.2`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` +``2.3`` ``-Python-3.7.2`` ``foss/2019a``, ``intel/2019a`` +``2.4`` ``-Python-3.7.2`` ``foss/2019a``, ``intel/2019a`` +``2.4`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` +======== ================== =============================================== .. _list_software_NeuroKit_817: @@ -19867,13 +20952,15 @@ version versionsuffix toolchain Nextflow is a reactive workflow framework and a programming DSL that eases writing computational pipelines with complex data -*homepage*: https://www.nextflow.io/ +*homepage*: https://www.nextflow.io =========== ========== version toolchain =========== ========== ``19.04.0`` ``system`` ``19.07.0`` ``system`` +``19.12.0`` ``system`` +``20.01.0`` ``system`` =========== ========== @@ -19979,6 +21066,22 @@ version toolchain ======= ================== +.. _list_software_ngspice_745: + +*ngspice* ++++++++++ + +Ngspice is a mixed-level/mixed-signal circuit simulator. Its code is based on three open source software packages: Spice3f5, Cider1b1 and Xspice. + +*homepage*: https://ngspice.sourceforge.net + +======= ============== +version toolchain +======= ============== +``31`` ``foss/2019b`` +======= ============== + + .. _list_software_NiBabel_653: *NiBabel* @@ -20172,6 +21275,7 @@ version toolchain ``8.9.4`` ``foss/2017a`` ``10.15.1`` ``foss/2018b`` ``10.15.3`` ``GCCcore/8.2.0`` +``12.16.1`` ``GCCcore/8.3.0`` =========== ================= @@ -20310,6 +21414,38 @@ version toolchain ========== ==================================== +.. _list_software_ntEdit_616: + +*ntEdit* +++++++++ + +ntEdit is a fast and scalable genomics application for polishing genome assembly drafts. + +*homepage*: https://github.com/bcgsc/ntEdit + +========= ====================================== +version toolchain +========= ====================================== +``1.3.1`` ``iccifort/2018.3.222-GCC-7.3.0-2.30`` +========= ====================================== + + +.. _list_software_ntHits_634: + +*ntHits* +++++++++ + +ntHits is a method for identifying repeats in high-throughput DNA sequencing data. + +*homepage*: https://github.com/bcgsc/ntHits + +========= ====================================== +version toolchain +========= ====================================== +``0.0.1`` ``iccifort/2018.3.222-GCC-7.3.0-2.30`` +========= ====================================== + + .. _list_software_numactl_756: *numactl* @@ -20339,18 +21475,19 @@ Numba is an Open Source NumPy-aware optimizing compiler for Python sponsored by *homepage*: https://numba.pydata.org/ -========== ================== =============================== -version versionsuffix toolchain -========== ================== =============================== -``0.24.0`` ``-Python-2.7.11`` ``intel/2016a`` -``0.24.0`` ``-Python-3.5.1`` ``intel/2016a`` -``0.26.0`` ``-Python-2.7.11`` ``intel/2016a`` -``0.32.0`` ``-Python-2.7.13`` ``intel/2017a`` -``0.37.0`` ``-Python-2.7.14`` ``foss/2018a``, ``intel/2017b`` -``0.37.0`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` -``0.43.1`` ``intel/2019a`` -``0.46.0`` ``foss/2019a`` -========== ================== =============================== +========== ================== ================================== +version versionsuffix toolchain +========== ================== ================================== +``0.24.0`` ``-Python-2.7.11`` ``intel/2016a`` +``0.24.0`` ``-Python-3.5.1`` ``intel/2016a`` +``0.26.0`` ``-Python-2.7.11`` ``intel/2016a`` +``0.32.0`` ``-Python-2.7.13`` ``intel/2017a`` +``0.37.0`` ``-Python-2.7.14`` ``foss/2018a``, ``intel/2017b`` +``0.37.0`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` +``0.43.1`` ``intel/2019a`` +``0.46.0`` ``foss/2019a`` +``0.47.0`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` +========== ================== ================================== .. _list_software_numexpr_783: @@ -20360,7 +21497,7 @@ version versionsuffix toolchain The numexpr package evaluates multiple-operator array expressions many times faster than NumPy can. It accepts the expression as a string, analyzes it, rewrites it more efficiently, and compiles it on the fly into code for its internal virtual machine (VM). Due to its integrated just-in-time (JIT) compiler, it does not require a compiler at runtime. -*homepage*: https://numexpr.readthedocs.io +*homepage*: https://numexpr.readthedocs.io/en/latest/ ========= ================== ================================== version versionsuffix toolchain @@ -20377,6 +21514,8 @@ version versionsuffix toolchain ``2.6.5`` ``-Python-2.7.15`` ``foss/2018b``, ``intel/2018b`` ``2.6.5`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b`` ``2.7.0`` ``intel/2019a`` +``2.7.1`` ``-Python-2.7.16`` ``intel/2019b`` +``2.7.1`` ``-Python-3.7.4`` ``foss/2019b`` ========= ================== ================================== @@ -20458,7 +21597,7 @@ version toolchain --- -:ref:`list_software_Oases_507` - :ref:`list_software_OBITools_747` - :ref:`list_software_OCaml_460` - :ref:`list_software_Octave_610` - :ref:`list_software_OMA_221` - :ref:`list_software_OOMPA_380` - :ref:`list_software_OPARI2_429` - :ref:`list_software_OpenBabel_872` - :ref:`list_software_OpenBLAS_692` - :ref:`list_software_OpenCoarrays_1238` - :ref:`list_software_OpenColorIO_1065` - :ref:`list_software_OpenCV_555` - :ref:`list_software_opencv_contrib_1499` - :ref:`list_software_OpenEXR_641` - :ref:`list_software_OpenFOAM_693` - :ref:`list_software_OpenFOAM-Extend_1354` - :ref:`list_software_OpenImageIO_1037` - :ref:`list_software_OpenJPEG_696` - :ref:`list_software_OpenKIM-API_890` - :ref:`list_software_openkim-models_1444` - :ref:`list_software_OpenMM_556` - :ref:`list_software_OpenMolcas_1009` - :ref:`list_software_OpenMPI_632` - :ref:`list_software_OpenNLP_636` - :ref:`list_software_OpenPGM_630` - :ref:`list_software_openpyxl_895` - :ref:`list_software_OpenRefine_1003` - :ref:`list_software_OpenSlide_899` - :ref:`list_software_openslide-python_1682` - :ref:`list_software_OpenSSL_644` - :ref:`list_software_OPERA_375` - :ref:`list_software_OptiType_830` - :ref:`list_software_OptiX_500` - :ref:`list_software_OR-Tools_735` - :ref:`list_software_ORCA_293` - :ref:`list_software_OrfM_372` - :ref:`list_software_OrthoFinder_1124` - :ref:`list_software_OrthoMCL_744` - :ref:`list_software_OSU-Micro-Benchmarks_1865` - :ref:`list_software_OTF2_283` - :ref:`list_software_ownCloud_843` - :ref:`list_software_oxford_asl_1073` +:ref:`list_software_Oases_507` - :ref:`list_software_OBITools_747` - :ref:`list_software_OCaml_460` - :ref:`list_software_occt_425` - :ref:`list_software_OCNet_441` - :ref:`list_software_Octave_610` - :ref:`list_software_OMA_221` - :ref:`list_software_OOMPA_380` - :ref:`list_software_OPARI2_429` - :ref:`list_software_OpenAI-Gym_886` - :ref:`list_software_OpenBabel_872` - :ref:`list_software_OpenBLAS_692` - :ref:`list_software_OpenCoarrays_1238` - :ref:`list_software_OpenColorIO_1065` - :ref:`list_software_OpenCV_555` - :ref:`list_software_opencv_contrib_1499` - :ref:`list_software_OpenEXR_641` - :ref:`list_software_OpenFOAM_693` - :ref:`list_software_OpenFOAM-Extend_1354` - :ref:`list_software_OpenImageIO_1037` - :ref:`list_software_OpenJPEG_696` - :ref:`list_software_OpenKIM-API_890` - :ref:`list_software_openkim-models_1444` - :ref:`list_software_OpenMM_556` - :ref:`list_software_OpenMolcas_1009` - :ref:`list_software_OpenMPI_632` - :ref:`list_software_OpenNLP_636` - :ref:`list_software_OpenPGM_630` - :ref:`list_software_OpenPIV_641` - :ref:`list_software_openpyxl_895` - :ref:`list_software_OpenPyXL_767` - :ref:`list_software_OpenRefine_1003` - :ref:`list_software_OpenSlide_899` - :ref:`list_software_openslide-python_1682` - :ref:`list_software_OpenSSL_644` - :ref:`list_software_OPERA_375` - :ref:`list_software_OptiType_830` - :ref:`list_software_OptiX_500` - :ref:`list_software_OR-Tools_735` - :ref:`list_software_orca_421` - :ref:`list_software_ORCA_293` - :ref:`list_software_OrfM_372` - :ref:`list_software_OrthoFinder_1124` - :ref:`list_software_OrthoMCL_744` - :ref:`list_software_Osi_299` - :ref:`list_software_OSU-Micro-Benchmarks_1865` - :ref:`list_software_OTF2_283` - :ref:`list_software_ownCloud_843` - :ref:`list_software_oxford_asl_1073` .. _list_software_Oases_507: @@ -20511,6 +21650,38 @@ version toolchain ========== ============== +.. _list_software_occt_425: + +*occt* +++++++ + +Open CASCADE Technology (OCCT) is an object-oriented C++ class library designed for rapid production of sophisticated domain-specific CAD/CAM/CAE applications. + +*homepage*: https://www.opencascade.com/ + +=========== ============== +version toolchain +=========== ============== +``7.3.0p4`` ``foss/2019b`` +=========== ============== + + +.. _list_software_OCNet_441: + +*OCNet* ++++++++ + +Generate and analyze Optimal Channel Networks (OCNs): oriented spanning trees reproducing all scaling features characteristic of real, natural river networks. As such, they can be used in a variety of numerical experiments in the fields of hydrology, ecology and epidemiology. + +*homepage*: https://cran.r-project.org/web/packages/OCNet + +========= ============= ============== +version versionsuffix toolchain +========= ============= ============== +``0.2.0`` ``-R-3.6.0`` ``foss/2019a`` +========= ============= ============== + + .. _list_software_Octave_610: *Octave* @@ -20518,7 +21689,7 @@ version toolchain GNU Octave is a high-level interpreted language, primarily intended for numerical computations. -*homepage*: http://www.gnu.org/software/octave/ +*homepage*: https://www.gnu.org/software/octave/ ========= ============= ================================================ version versionsuffix toolchain @@ -20529,6 +21700,7 @@ version versionsuffix toolchain ``4.2.1`` ``-mt`` ``intel/2017a`` ``4.2.2`` ``foss/2018a`` ``4.4.1`` ``foss/2018b`` +``5.1.0`` ``foss/2019a``, ``foss/2019b`` ========= ============= ================================================ @@ -20581,6 +21753,22 @@ version toolchain ========= ================= +.. _list_software_OpenAI-Gym_886: + +*OpenAI-Gym* +++++++++++++ + +A toolkit for developing and comparing reinforcement learning algorithms. + +*homepage*: https://gym.openai.com + +========== ================= ============== +version versionsuffix toolchain +========== ================= ============== +``0.17.1`` ``-Python-3.7.4`` ``foss/2019b`` +========== ================= ============== + + .. _list_software_OpenBabel_872: *OpenBabel* @@ -20588,7 +21776,7 @@ version toolchain Open Babel is a chemical toolbox designed to speak the many languages of chemical data. It's an open, collaborative project allowing anyone to search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas. -*homepage*: http://openbabel.org +*homepage*: https://openbabel.org ========= ================== =============== version versionsuffix toolchain @@ -20597,6 +21785,8 @@ version versionsuffix toolchain ``2.4.1`` ``-Python-2.7.14`` ``intel/2017b`` ``2.4.1`` ``-Python-2.7.15`` ``intel/2018b`` ``2.4.1`` ``-Python-3.6.6`` ``intel/2018b`` +``2.4.1`` ``-Python-3.7.2`` ``intel/2019a`` +``3.0.0`` ``-Python-3.7.4`` ``gompi/2019b`` ========= ================== =============== @@ -20607,7 +21797,7 @@ version versionsuffix toolchain OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version. -*homepage*: http://xianyi.github.com/OpenBLAS/ +*homepage*: https://xianyi.github.com/OpenBLAS/ ========== ================= ========================================================== version versionsuffix toolchain @@ -20629,6 +21819,7 @@ version versionsuffix toolchain ``0.3.5`` ``GCC/8.2.0-2.31.1`` ``0.3.6`` ``GCC/8.3.0-2.32`` ``0.3.7`` ``GCC/8.3.0`` +``0.3.8`` ``GCC/9.2.0`` ========== ================= ========================================================== @@ -20673,7 +21864,7 @@ version toolchain OpenCV (Open Source Computer Vision Library) is an open source computer vision and machine learning software library. OpenCV was built to provide a common infrastructure for computer vision applications and to accelerate the use of machine perception in the commercial products. -*homepage*: http://opencv.org/ +*homepage*: https://opencv.org/ ========== ================== ================================================================ version versionsuffix toolchain @@ -20691,6 +21882,7 @@ version versionsuffix toolchain ``3.4.7`` ``-Python-3.7.2`` ``foss/2019a``, ``fosscuda/2019a`` ``4.0.1`` ``-Python-2.7.15`` ``foss/2018b`` ``4.0.1`` ``-Python-3.6.6`` ``foss/2018b`` +``4.2.0`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` ========== ================== ================================================================ @@ -20701,7 +21893,7 @@ version versionsuffix toolchain OpenCV (Open Source Computer Vision Library) is an open source computer vision and machine learning software library. OpenCV was built to provide a common infrastructure for computer vision applications and to accelerate the use of machine perception in the commercial products. -*homepage*: http://opencv.org/ +*homepage*: https://opencv.org/ ========= ================= ============== version versionsuffix toolchain @@ -20742,7 +21934,7 @@ version toolchain ================ ================================================ ``2.2.2`` ``intel/2016a``, ``intel/2017a`` ``2.2.x`` ``intel/2019a`` -``2.3.1`` ``intel/2017a`` +``2.3.1`` ``intel/2017a``, ``intel/2019b`` ``2.4.0`` ``intel/2017a``, ``intel/2019a`` ``3.0.0`` ``foss/2016a`` ``3.0.1`` ``intel/2016b``, ``intel/2018a`` @@ -20758,7 +21950,7 @@ version toolchain ``v1806`` ``foss/2018b`` ``v1812`` ``foss/2018b`` ``v1906`` ``foss/2019b`` -``v1912`` ``foss/2019b`` +``v1912`` ``foss/2019b``, ``intel/2019b`` ================ ================================================ @@ -20771,14 +21963,15 @@ OpenFOAM is a free, open source CFD software package. OpenFOAM has an extensive *homepage*: http://www.extend-project.de/ -======= ================== ================================= -version versionsuffix toolchain -======= ================== ================================= -``3.1`` ``gimkl/2.11.5`` -``3.2`` ``gimkl/2.11.5``, ``intel/2016a`` -``4.0`` ``intel/2017a`` -``4.0`` ``-Python-2.7.16`` ``intel/2019b`` -======= ================== ================================= +================ ================== ================================= +version versionsuffix toolchain +================ ================== ================================= +``3.1`` ``gimkl/2.11.5`` +``3.2`` ``gimkl/2.11.5``, ``intel/2016a`` +``4.0`` ``intel/2017a`` +``4.0`` ``-Python-2.7.16`` ``intel/2019b`` +``4.1-20191120`` ``-Python-2.7.16`` ``intel/2019b`` +================ ================== ================================= .. _list_software_OpenImageIO_1037: @@ -20844,11 +22037,11 @@ Open Knowledgebase of Interatomic Models. OpenKIM is an API and a collection of *homepage*: https://openkim.org/ -============ =============================== -version toolchain -============ =============================== -``20190725`` ``foss/2019a``, ``intel/2019a`` -============ =============================== +============ ================================================================ +version toolchain +============ ================================================================ +``20190725`` ``foss/2019a``, ``foss/2019b``, ``intel/2019a``, ``intel/2019b`` +============ ================================================================ .. _list_software_OpenMM_556: @@ -20963,6 +22156,22 @@ version toolchain =========== ============================================================================================================================================================================= +.. _list_software_OpenPIV_641: + +*OpenPIV* ++++++++++ + +OpenPIV is an open source Particle Image Velocimetry analysis software + +*homepage*: http://www.openpiv.net + +========== ================= =============== +version versionsuffix toolchain +========== ================= =============== +``0.21.8`` ``-Python-3.7.4`` ``intel/2019b`` +========== ================= =============== + + .. _list_software_openpyxl_895: *openpyxl* @@ -20979,6 +22188,22 @@ version toolchain ========= ================= +.. _list_software_OpenPyXL_767: + +*OpenPyXL* +++++++++++ + +A Python library to read/write Excel 2010 xlsx/xlsm files + +*homepage*: https://openpyxl.readthedocs.io + +========= ================= +version toolchain +========= ================= +``2.6.4`` ``GCCcore/8.3.0`` +========= ================= + + .. _list_software_OpenRefine_1003: *OpenRefine* @@ -21118,6 +22343,22 @@ version versionsuffix toolchain ======= ================= ============== +.. _list_software_orca_421: + +*orca* +++++++ + +Orca is an Electron app that generates images and reports of Plotly things like plotly.js graphs, dash apps, dashboards from the command line. + +*homepage*: https://github.com/plotly/orca + +========= ================= +version toolchain +========= ================= +``1.3.0`` ``GCCcore/8.3.0`` +========= ================= + + .. _list_software_ORCA_293: *ORCA* @@ -21165,12 +22406,14 @@ OrthoFinder is a fast, accurate and comprehensive platform for comparative genom *homepage*: https://github.com/davidemms/OrthoFinder -========= ================== =============== -version versionsuffix toolchain -========= ================== =============== -``2.2.7`` ``-Python-2.7.14`` ``intel/2018a`` -``2.3.3`` ``-Python-2.7.15`` ``intel/2018b`` -========= ================== =============== +========== ================== =============== +version versionsuffix toolchain +========== ================== =============== +``2.2.7`` ``-Python-2.7.14`` ``intel/2018a`` +``2.3.3`` ``-Python-2.7.15`` ``intel/2018b`` +``2.3.8`` ``-Python-2.7.16`` ``foss/2019b`` +``2.3.11`` ``-Python-3.7.4`` ``intel/2019b`` +========== ================== =============== .. _list_software_OrthoMCL_744: @@ -21190,14 +22433,30 @@ version versionsuffix toolchain ========= ================ =============== -.. _list_software_OSU-Micro-Benchmarks_1865: +.. _list_software_Osi_299: -*OSU-Micro-Benchmarks* -++++++++++++++++++++++ +*Osi* ++++++ -OSU Micro-Benchmarks +Osi (Open Solver Interface) provides an abstract base class to a generic linear programming (LP) solver, along with derived classes for specific solvers. Many applications may be able to use the Osi to insulate themselves from a specific LP solver. That is, programs written to the OSI standard may be linked to any solver with an OSI interface and should produce correct results. The OSI has been significantly extended compared to its first incarnation. Currently, the OSI supports linear programming solvers and has rudimentary support for integer programming. -*homepage*: http://mvapich.cse.ohio-state.edu/benchmarks/ +*homepage*: https://github.com/coin-or/Osi + +=========== ================= +version toolchain +=========== ================= +``0.108.5`` ``GCCcore/7.3.0`` +=========== ================= + + +.. _list_software_OSU-Micro-Benchmarks_1865: + +*OSU-Micro-Benchmarks* +++++++++++++++++++++++ + +OSU Micro-Benchmarks + +*homepage*: http://mvapich.cse.ohio-state.edu/benchmarks/ ========= ============================== version toolchain @@ -21263,7 +22522,7 @@ version versionsuffix toolchain --- -:ref:`list_software_p11-kit_583` - :ref:`list_software_p4est_496` - :ref:`list_software_p4vasp_606` - :ref:`list_software_p7zip_506` - :ref:`list_software_packmol_743` - :ref:`list_software_PAML_298` - :ref:`list_software_pandas_631` - :ref:`list_software_pandas-datareader_1713` - :ref:`list_software_PANDAseq_685` - :ref:`list_software_Pandoc_597` - :ref:`list_software_Pango_501` - :ref:`list_software_PAPI_298` - :ref:`list_software_parallel_845` - :ref:`list_software_parallel-fastq-dump_1916` - :ref:`list_software_ParallelIO_965` - :ref:`list_software_parasail_845` - :ref:`list_software_Paraver_721` - :ref:`list_software_ParaView_799` - :ref:`list_software_PARI-GP_496` - :ref:`list_software_ParmEd_569` - :ref:`list_software_ParMETIS_677` - :ref:`list_software_ParMGridGen_1040` - :ref:`list_software_pasta_537` - :ref:`list_software_PaStiX_569` - :ref:`list_software_patchelf_839` - :ref:`list_software_path.py_708` - :ref:`list_software_pbbam_514` - :ref:`list_software_pbcopper_859` - :ref:`list_software_pbdagcon_830` - :ref:`list_software_pbmm2_478` - :ref:`list_software_pbs_python_1094` - :ref:`list_software_PBSuite_668` - :ref:`list_software_PCAngsd_640` - :ref:`list_software_PCC_214` - :ref:`list_software_PCL_223` - :ref:`list_software_PCMSolver_859` - :ref:`list_software_PCRaster_772` - :ref:`list_software_PCRE_298` - :ref:`list_software_PCRE2_348` - :ref:`list_software_PDT_232` - :ref:`list_software_PEAR_296` - :ref:`list_software_Perl_403` - :ref:`list_software_perl-app-cpanminus_1820` - :ref:`list_software_Perl4-CoreLibs_1287` - :ref:`list_software_PETSc_415` - :ref:`list_software_petsc4py_828` - :ref:`list_software_pftoolsV3_912` - :ref:`list_software_pFUnit_598` - :ref:`list_software_PGDSpider_834` - :ref:`list_software_PGI_224` - :ref:`list_software_PHASE_369` - :ref:`list_software_PHAST_384` - :ref:`list_software_PheWAS_520` - :ref:`list_software_PhiPack_672` - :ref:`list_software_PHLAT_377` - :ref:`list_software_phono3py_832` - :ref:`list_software_phonopy_781` - :ref:`list_software_PHYLIP_470` - :ref:`list_software_PhyloBayes-MPI_1299` - :ref:`list_software_phylokit_884` - :ref:`list_software_phylonaut_996` - :ref:`list_software_PhyML_458` - :ref:`list_software_phyx_457` - :ref:`list_software_picard_627` - :ref:`list_software_pigz_442` - :ref:`list_software_PIL_229` - :ref:`list_software_PileOMeth_871` - :ref:`list_software_Pillow_631` - :ref:`list_software_Pillow-SIMD_977` - :ref:`list_software_Pilon_514` - :ref:`list_software_PIMS_313` - :ref:`list_software_Pindel_604` - :ref:`list_software_pip_329` - :ref:`list_software_Pisces_615` - :ref:`list_software_piSvM_495` - :ref:`list_software_piSvM-JSC_764` - :ref:`list_software_pixman_653` - :ref:`list_software_pizzly_690` - :ref:`list_software_pkg-config_997` - :ref:`list_software_pkgconfig_952` - :ref:`list_software_PlaScope_791` - :ref:`list_software_PLAST_388` - :ref:`list_software_Platanus_840` - :ref:`list_software_Platypus_866` - :ref:`list_software_plc_319` - :ref:`list_software_PLINK_382` - :ref:`list_software_PLINKSEQ_615` - :ref:`list_software_Ploticus_851` - :ref:`list_software_plotly_676` - :ref:`list_software_plotly.py_955` - :ref:`list_software_PLplot_603` - :ref:`list_software_PLUMED_455` - :ref:`list_software_PLY_245` - :ref:`list_software_PMIx_350` - :ref:`list_software_PnetCDF_612` - :ref:`list_software_pocl_430` - :ref:`list_software_pomkl_547` - :ref:`list_software_pompi_549` - :ref:`list_software_poppler_770` - :ref:`list_software_popt_451` - :ref:`list_software_Porechop_832` - :ref:`list_software_poretools_999` - :ref:`list_software_Postgres-XL_1064` - :ref:`list_software_PostgreSQL_980` - :ref:`list_software_POT_243` - :ref:`list_software_POV-Ray_590` - :ref:`list_software_PPfold_581` - :ref:`list_software_ppl_332` - :ref:`list_software_pplacer_743` - :ref:`list_software_pplpy_565` - :ref:`list_software_PRANK_380` - :ref:`list_software_PRC_229` - :ref:`list_software_preseq_656` - :ref:`list_software_Primer3_674` - :ref:`list_software_PRINSEQ_546` - :ref:`list_software_printproto_1121` - :ref:`list_software_PRISMS-PF_673` - :ref:`list_software_ProbABEL_679` - :ref:`list_software_prodigal_850` - :ref:`list_software_PROJ_315` - :ref:`list_software_ProjectQ_808` - :ref:`list_software_prokka_648` - :ref:`list_software_prompt-toolkit_1493` - :ref:`list_software_proovread_978` - :ref:`list_software_propy_570` - :ref:`list_software_Proteinortho_1293` - :ref:`list_software_protobuf_881` - :ref:`list_software_protobuf-python_1600` - :ref:`list_software_pscom_546` - :ref:`list_software_PSI_236` - :ref:`list_software_PSI4_288` - :ref:`list_software_psmc_435` - :ref:`list_software_psmpi_553` - :ref:`list_software_psmpi2_603` - :ref:`list_software_PSolver_715` - :ref:`list_software_PSORTb_506` - :ref:`list_software_psrecord_866` - :ref:`list_software_pstoedit_876` - :ref:`list_software_psutil_673` - :ref:`list_software_psycopg2_823` - :ref:`list_software_ptemcee_739` - :ref:`list_software_PTESFinder_916` - :ref:`list_software_pubtcrs_771` - :ref:`list_software_pullseq_774` - :ref:`list_software_py_233` - :ref:`list_software_py-cpuinfo_1034` - :ref:`list_software_PyAMG_414` - :ref:`list_software_PyAPS3_480` - :ref:`list_software_pybedtools_1093` - :ref:`list_software_pyBigWig_802` - :ref:`list_software_pybind11_744` - :ref:`list_software_PyCairo_695` - :ref:`list_software_PyCharm_692` - :ref:`list_software_pycma_538` - :ref:`list_software_PyCogent_809` - :ref:`list_software_PyCUDA_486` - :ref:`list_software_PyDatastream_1231` - :ref:`list_software_pydicom_757` - :ref:`list_software_pydlpoly_893` - :ref:`list_software_pyEGA3_489` - :ref:`list_software_pyenchant_970` - :ref:`list_software_PyFFmpeg_766` - :ref:`list_software_pyFFTW_544` - :ref:`list_software_pyfits_671` - :ref:`list_software_PyFMI_421` - :ref:`list_software_PyFR_353` - :ref:`list_software_pygccxml_871` - :ref:`list_software_pyGIMLi_635` - :ref:`list_software_Pygments_855` - :ref:`list_software_PyGObject_871` - :ref:`list_software_pygrib_653` - :ref:`list_software_PyGTK_431` - :ref:`list_software_PyGTS_439` - :ref:`list_software_PyGWAS_507` - :ref:`list_software_pyhdf_539` - :ref:`list_software_pyiron_673` - :ref:`list_software_Pyke3_460` - :ref:`list_software_Pylint_640` - :ref:`list_software_pymatgen_869` - :ref:`list_software_pymatgen-db_1112` - :ref:`list_software_pymbar_651` - :ref:`list_software_pymemcache_1052` - :ref:`list_software_PyNAST_511` - :ref:`list_software_Pyomo_532` - :ref:`list_software_PyOpenGL_750` - :ref:`list_software_pyplusplus_1137` - :ref:`list_software_pyproj_676` - :ref:`list_software_pyqstem_787` - :ref:`list_software_PyQt_398` - :ref:`list_software_PyQt5_451` - :ref:`list_software_PyQtGraph_896` - :ref:`list_software_PyRETIS_592` - :ref:`list_software_pyringe_766` - :ref:`list_software_Pyro4_478` - :ref:`list_software_Pysam_522` - :ref:`list_software_pyScaf_614` - :ref:`list_software_PySCF_421` - :ref:`list_software_pyshp_564` - :ref:`list_software_Pysolar_746` - :ref:`list_software_pysqlite_891` - :ref:`list_software_PyStan_607` - :ref:`list_software_pystran_785` - :ref:`list_software_PyTables_804` - :ref:`list_software_pytest_681` - :ref:`list_software_PYTHIA_463` - :ref:`list_software_Python_642` - :ref:`list_software_python-igraph_1354` - :ref:`list_software_python-Levenshtein_1876` - :ref:`list_software_python-parasail_1564` - :ref:`list_software_pythran_774` - :ref:`list_software_PyTorch_713` - :ref:`list_software_PyYAML_508` - :ref:`list_software_PyZMQ_449` +:ref:`list_software_p11-kit_583` - :ref:`list_software_p4est_496` - :ref:`list_software_p4vasp_606` - :ref:`list_software_p7zip_506` - :ref:`list_software_packmol_743` - :ref:`list_software_PAML_298` - :ref:`list_software_pandas_631` - :ref:`list_software_pandas-datareader_1713` - :ref:`list_software_PANDAseq_685` - :ref:`list_software_Pandoc_597` - :ref:`list_software_Pango_501` - :ref:`list_software_PAPI_298` - :ref:`list_software_parallel_845` - :ref:`list_software_parallel-fastq-dump_1916` - :ref:`list_software_ParallelIO_965` - :ref:`list_software_parasail_845` - :ref:`list_software_Paraver_721` - :ref:`list_software_ParaView_799` - :ref:`list_software_PARI-GP_496` - :ref:`list_software_ParmEd_569` - :ref:`list_software_ParMETIS_677` - :ref:`list_software_ParMGridGen_1040` - :ref:`list_software_PartitionFinder_1554` - :ref:`list_software_pasta_537` - :ref:`list_software_PaStiX_569` - :ref:`list_software_patchelf_839` - :ref:`list_software_path.py_708` - :ref:`list_software_pauvre_659` - :ref:`list_software_pbbam_514` - :ref:`list_software_pbcopper_859` - :ref:`list_software_pbdagcon_830` - :ref:`list_software_pbmm2_478` - :ref:`list_software_pbs_python_1094` - :ref:`list_software_PBSuite_668` - :ref:`list_software_PCAngsd_640` - :ref:`list_software_PCC_214` - :ref:`list_software_PCL_223` - :ref:`list_software_PCMSolver_859` - :ref:`list_software_PCRaster_772` - :ref:`list_software_PCRE_298` - :ref:`list_software_PCRE2_348` - :ref:`list_software_PDT_232` - :ref:`list_software_PEAR_296` - :ref:`list_software_Perl_403` - :ref:`list_software_perl-app-cpanminus_1820` - :ref:`list_software_Perl4-CoreLibs_1287` - :ref:`list_software_PETSc_415` - :ref:`list_software_petsc4py_828` - :ref:`list_software_pftoolsV3_912` - :ref:`list_software_pFUnit_598` - :ref:`list_software_PGDSpider_834` - :ref:`list_software_PGI_224` - :ref:`list_software_PHASE_369` - :ref:`list_software_PHAST_384` - :ref:`list_software_PheWAS_520` - :ref:`list_software_PhiPack_672` - :ref:`list_software_PHLAT_377` - :ref:`list_software_phono3py_832` - :ref:`list_software_phonopy_781` - :ref:`list_software_PHYLIP_470` - :ref:`list_software_PhyloBayes-MPI_1299` - :ref:`list_software_phylokit_884` - :ref:`list_software_phylonaut_996` - :ref:`list_software_PhyML_458` - :ref:`list_software_phyx_457` - :ref:`list_software_picard_627` - :ref:`list_software_pigz_442` - :ref:`list_software_PIL_229` - :ref:`list_software_PileOMeth_871` - :ref:`list_software_Pillow_631` - :ref:`list_software_Pillow-SIMD_977` - :ref:`list_software_Pilon_514` - :ref:`list_software_PIMS_313` - :ref:`list_software_Pindel_604` - :ref:`list_software_pip_329` - :ref:`list_software_Pisces_615` - :ref:`list_software_piSvM_495` - :ref:`list_software_piSvM-JSC_764` - :ref:`list_software_pixman_653` - :ref:`list_software_pizzly_690` - :ref:`list_software_pkg-config_997` - :ref:`list_software_pkgconfig_952` - :ref:`list_software_PlaScope_791` - :ref:`list_software_PLAST_388` - :ref:`list_software_Platanus_840` - :ref:`list_software_Platypus_866` - :ref:`list_software_plc_319` - :ref:`list_software_PLINK_382` - :ref:`list_software_PLINKSEQ_615` - :ref:`list_software_Ploticus_851` - :ref:`list_software_plotly_676` - :ref:`list_software_plotly.py_955` - :ref:`list_software_PLplot_603` - :ref:`list_software_PLUMED_455` - :ref:`list_software_PLY_245` - :ref:`list_software_PMIx_350` - :ref:`list_software_PnetCDF_612` - :ref:`list_software_pocl_430` - :ref:`list_software_polymake_866` - :ref:`list_software_pomkl_547` - :ref:`list_software_pompi_549` - :ref:`list_software_poppler_770` - :ref:`list_software_popt_451` - :ref:`list_software_Porechop_832` - :ref:`list_software_poretools_999` - :ref:`list_software_Postgres-XL_1064` - :ref:`list_software_PostgreSQL_980` - :ref:`list_software_POT_243` - :ref:`list_software_POV-Ray_590` - :ref:`list_software_PPfold_581` - :ref:`list_software_ppl_332` - :ref:`list_software_pplacer_743` - :ref:`list_software_pplpy_565` - :ref:`list_software_PRANK_380` - :ref:`list_software_PRC_229` - :ref:`list_software_preseq_656` - :ref:`list_software_pretty-yaml_1160` - :ref:`list_software_Primer3_674` - :ref:`list_software_PRINSEQ_546` - :ref:`list_software_printproto_1121` - :ref:`list_software_PRISMS-PF_673` - :ref:`list_software_ProbABEL_679` - :ref:`list_software_prodigal_850` - :ref:`list_software_PROJ_315` - :ref:`list_software_ProjectQ_808` - :ref:`list_software_prokka_648` - :ref:`list_software_prompt-toolkit_1493` - :ref:`list_software_proovread_978` - :ref:`list_software_propy_570` - :ref:`list_software_Proteinortho_1293` - :ref:`list_software_protobuf_881` - :ref:`list_software_protobuf-python_1600` - :ref:`list_software_PRSice_550` - :ref:`list_software_pscom_546` - :ref:`list_software_PSI_236` - :ref:`list_software_PSI4_288` - :ref:`list_software_psmc_435` - :ref:`list_software_psmpi_553` - :ref:`list_software_psmpi2_603` - :ref:`list_software_PSolver_715` - :ref:`list_software_PSORTb_506` - :ref:`list_software_psrecord_866` - :ref:`list_software_pstoedit_876` - :ref:`list_software_psutil_673` - :ref:`list_software_psycopg2_823` - :ref:`list_software_ptemcee_739` - :ref:`list_software_PTESFinder_916` - :ref:`list_software_pubtcrs_771` - :ref:`list_software_pullseq_774` - :ref:`list_software_py_233` - :ref:`list_software_py-cpuinfo_1034` - :ref:`list_software_PyAMG_414` - :ref:`list_software_PyAPS3_480` - :ref:`list_software_pybedtools_1093` - :ref:`list_software_pyBigWig_802` - :ref:`list_software_pybind11_744` - :ref:`list_software_PyCairo_695` - :ref:`list_software_PyCharm_692` - :ref:`list_software_pycma_538` - :ref:`list_software_pycodestyle_1205` - :ref:`list_software_PyCogent_809` - :ref:`list_software_PyCUDA_486` - :ref:`list_software_PyDatastream_1231` - :ref:`list_software_pydicom_757` - :ref:`list_software_pydlpoly_893` - :ref:`list_software_pydot_560` - :ref:`list_software_pyEGA3_489` - :ref:`list_software_pyenchant_970` - :ref:`list_software_PyFFmpeg_766` - :ref:`list_software_pyFFTW_544` - :ref:`list_software_pyfits_671` - :ref:`list_software_PyFMI_421` - :ref:`list_software_PyFR_353` - :ref:`list_software_pygccxml_871` - :ref:`list_software_pyGIMLi_635` - :ref:`list_software_Pygments_855` - :ref:`list_software_PyGObject_871` - :ref:`list_software_pygraphviz_1108` - :ref:`list_software_pygrib_653` - :ref:`list_software_PyGTK_431` - :ref:`list_software_PyGTS_439` - :ref:`list_software_PyGWAS_507` - :ref:`list_software_pyhdf_539` - :ref:`list_software_pyiron_673` - :ref:`list_software_Pyke3_460` - :ref:`list_software_pylift_664` - :ref:`list_software_Pylint_640` - :ref:`list_software_pymatgen_869` - :ref:`list_software_pymatgen-db_1112` - :ref:`list_software_pymbar_651` - :ref:`list_software_PyMC3_396` - :ref:`list_software_pymemcache_1052` - :ref:`list_software_PyNAST_511` - :ref:`list_software_Pyomo_532` - :ref:`list_software_PyOpenGL_750` - :ref:`list_software_pyparsing_989` - :ref:`list_software_pyplusplus_1137` - :ref:`list_software_pyproj_676` - :ref:`list_software_pyqstem_787` - :ref:`list_software_PyQt_398` - :ref:`list_software_PyQt5_451` - :ref:`list_software_PyQtGraph_896` - :ref:`list_software_PyRe_384` - :ref:`list_software_PyRETIS_592` - :ref:`list_software_pyringe_766` - :ref:`list_software_Pyro4_478` - :ref:`list_software_Pysam_522` - :ref:`list_software_pyScaf_614` - :ref:`list_software_PySCF_421` - :ref:`list_software_pyshp_564` - :ref:`list_software_Pysolar_746` - :ref:`list_software_pysqlite_891` - :ref:`list_software_PyStan_607` - :ref:`list_software_pystran_785` - :ref:`list_software_PyTables_804` - :ref:`list_software_pytest_681` - :ref:`list_software_PYTHIA_463` - :ref:`list_software_Python_642` - :ref:`list_software_python-igraph_1354` - :ref:`list_software_python-Levenshtein_1876` - :ref:`list_software_python-parasail_1564` - :ref:`list_software_python-weka-wrapper3_2008` - :ref:`list_software_pythran_774` - :ref:`list_software_PyTorch_713` - :ref:`list_software_PyTorch-Geometric_1685` - :ref:`list_software_PyYAML_508` - :ref:`list_software_PyZMQ_449` .. _list_software_p11-kit_583: @@ -21464,6 +22723,7 @@ version toolchain ``1.41.1`` ``foss/2018a``, ``intel/2018a`` ``1.42.4`` ``foss/2018b``, ``fosscuda/2018b`` ``1.43.0`` ``GCCcore/8.2.0`` +``1.44.7`` ``GCCcore/8.3.0`` =========== ================================== @@ -21555,12 +22815,13 @@ parasail is a SIMD C (C99) library containing implementations of the Smith-Wate *homepage*: https://github.com/jeffdaily/parasail -======= =============== -version toolchain -======= =============== -``2.2`` ``intel/2018a`` -``2.4`` ``foss/2018b`` -======= =============== +========= =============== +version toolchain +========= =============== +``2.2`` ``intel/2018a`` +``2.4`` ``foss/2018b`` +``2.4.1`` ``intel/2019b`` +========= =============== .. _list_software_Paraver_721: @@ -21598,7 +22859,7 @@ version versionsuffix toolchain ``5.3.0`` ``-mpi`` ``foss/2016b`` ``5.4.1`` ``-mpi`` ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``intel/2017a``, ``intel/2017b``, ``intel/2018a`` ``5.5.2`` ``-Python-2.7.15-mpi`` ``foss/2018b`` -``5.6.2`` ``-Python-3.7.4-mpi`` ``foss/2019b`` +``5.6.2`` ``-Python-3.7.4-mpi`` ``foss/2019b``, ``intel/2019b`` ========= ====================== ================================================================================================= @@ -21643,11 +22904,11 @@ ParMETIS is an MPI-based parallel library that implements a variety of algorithm *homepage*: http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview -========= ========================================================================================================================================================================================================================================================================= -version toolchain -========= ========================================================================================================================================================================================================================================================================= -``4.0.3`` ``foss/2016a``, ``foss/2016b``, ``foss/2017a``, ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``gimkl/2.11.5``, ``gompi/2019a``, ``iimpi/2019a``, ``iimpi/2019b``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b`` -========= ========================================================================================================================================================================================================================================================================= +========= ========================================================================================================================================================================================================================================================================================== +version toolchain +========= ========================================================================================================================================================================================================================================================================================== +``4.0.3`` ``foss/2016a``, ``foss/2016b``, ``foss/2017a``, ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``gimkl/2.11.5``, ``gompi/2019a``, ``gompi/2019b``, ``iimpi/2019a``, ``iimpi/2019b``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b`` +========= ========================================================================================================================================================================================================================================================================================== .. _list_software_ParMGridGen_1040: @@ -21666,6 +22927,22 @@ version toolchain ======= =================================================================== +.. _list_software_PartitionFinder_1554: + +*PartitionFinder* ++++++++++++++++++ + +PartitionFinder 2 is a Python program for simultaneously choosing partitioning schemes and models of molecular evolution for phylogenetic analyses of DNA, protein, and morphological data. You can PartitionFinder 2 before running a phylogenetic analysis, in order to decide how to divide up your sequence data into separate blocks before analysis, and to simultaneously perform model selection on each of those blocks. + +*homepage*: https://www.robertlanfear.com/partitionfinder + +========= ================== =============== +version versionsuffix toolchain +========= ================== =============== +``2.1.1`` ``-Python-2.7.16`` ``intel/2019b`` +========= ================== =============== + + .. _list_software_pasta_537: *pasta* @@ -21736,6 +23013,22 @@ version versionsuffix toolchain ========= ================== =============================== +.. _list_software_pauvre_659: + +*pauvre* +++++++++ + +Tools for plotting Oxford Nanopore and other long-read data + +*homepage*: https://github.com/conchoecia/pauvre + +========== ================= =============== +version versionsuffix toolchain +========== ================= =============== +``0.1923`` ``-Python-3.7.4`` ``intel/2019b`` +========== ================= =============== + + .. _list_software_pbbam_514: *pbbam* @@ -22075,6 +23368,8 @@ version versionsuffix toolchain ``3.9.3`` ``foss/2018a``, ``intel/2018a`` ``3.11.0`` ``-downloaded-deps`` ``foss/2018b`` ``3.11.1`` ``foss/2019a``, ``intel/2019a`` +``3.12.3`` ``foss/2019b`` +``3.12.4`` ``foss/2019b``, ``intel/2019b`` ========== ==================== =============================== @@ -22173,6 +23468,7 @@ version versionsuffix toolchain ``19.1`` ``-GCC-8.2.0-2.31.1`` ``system`` ``19.4`` ``-GCC-8.2.0-2.31.1`` ``system`` ``19.7`` ``-GCC-8.3.0-2.32`` ``system`` +``19.10`` ``-GCC-8.3.0-2.32`` ``system`` ========= ======================= ========== @@ -22401,7 +23697,7 @@ version toolchain A set of tools (in Java) for working with next generation sequencing data in the BAM format. -*homepage*: http://sourceforge.net/projects/picard +*homepage*: https://sourceforge.net/projects/picard =========== =================== ========== version versionsuffix toolchain @@ -22427,6 +23723,7 @@ version versionsuffix toolchain ``2.18.17`` ``-Java-1.8`` ``system`` ``2.18.27`` ``-Java-1.8`` ``system`` ``2.21.1`` ``-Java-11`` ``system`` +``2.21.6`` ``-Java-11`` ``system`` =========== =================== ========== @@ -22439,13 +23736,13 @@ pigz, which stands for parallel implementation of gzip, is a fully functional *homepage*: https://zlib.net/pigz/ -========= ======================================================================= -version toolchain -========= ======================================================================= -``2.3.3`` ``foss/2016b`` -``2.3.4`` ``GCCcore/6.4.0`` -``2.4`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``foss/2018a`` -========= ======================================================================= +========= ========================================================================================== +version toolchain +========= ========================================================================================== +``2.3.3`` ``foss/2016b`` +``2.3.4`` ``GCCcore/6.4.0`` +``2.4`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``foss/2018a`` +========= ========================================================================================== .. _list_software_PIL_229: @@ -22702,7 +23999,7 @@ version toolchain ``0.28`` ``GCC/4.8.2``, ``GCC/4.9.2``, ``GNU/4.9.3-2.25`` ``0.29`` ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a`` ``0.29.1`` ``GCCcore/4.9.3``, ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2017a``, ``gimkl/2017a``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a`` -``0.29.2`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``intel/2017a``, ``system`` +``0.29.2`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``intel/2017a``, ``system`` ========== =========================================================================================================================================================================== @@ -22945,7 +24242,7 @@ version versionsuffix toolchain ``2.5.1`` ``foss/2019a``, ``intel/2018b`` ``2.5.1`` ``-PathCV`` ``intel/2018b`` ``2.5.2`` ``-Python-3.7.2`` ``intel/2019a`` -``2.5.3`` ``-Python-3.7.4`` ``intel/2019b`` +``2.5.3`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` ``2.5b`` ``-Python-2.7.14`` ``intel/2018a`` ========= ================== ================================================ @@ -22979,7 +24276,9 @@ Process Management for Exascale Environments PMI Exascale (PMIx) represents an a version toolchain ========= ======================================================= ``1.2.5`` ``GCCcore/6.4.0`` -``2.1.3`` ``GCCcore/7.3.0`` +``2.1.3`` ``GCCcore/7.2.0``, ``GCCcore/7.3.0`` +``2.2.1`` ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` +``2.2.3`` ``GCCcore/7.2.0``, ``GCCcore/7.3.0`` ``3.0.1`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` ``3.0.2`` ``GCCcore/8.2.0`` ``3.1.1`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` @@ -23023,6 +24322,22 @@ version toolchain ======= ================================ +.. _list_software_polymake_866: + +*polymake* +++++++++++ + +polymake is open source software for research in polyhedral geometry. It deals with polytopes, polyhedra and fans as well as simplicial complexes, matroids, graphs, tropical hypersurfaces, and other objects. + +*homepage*: https://polymake.org + +========= ============== +version toolchain +========= ============== +``4.0r1`` ``foss/2019b`` +========= ============== + + .. _list_software_pomkl_547: *pomkl* @@ -23101,12 +24416,13 @@ Porechop is a tool for finding and removing adapters from Oxford Nanopore reads. *homepage*: https://github.com/rrwick/Porechop -========= ================= ============== -version versionsuffix toolchain -========= ================= ============== -``0.2.3`` ``-Python-3.5.2`` ``foss/2016b`` -``0.2.4`` ``-Python-3.6.6`` ``foss/2018b`` -========= ================= ============== +========= ================= =============== +version versionsuffix toolchain +========= ================= =============== +``0.2.3`` ``-Python-3.5.2`` ``foss/2016b`` +``0.2.4`` ``-Python-3.6.6`` ``foss/2018b`` +``0.2.4`` ``-Python-3.7.4`` ``intel/2019b`` +========= ================= =============== .. _list_software_poretools_999: @@ -23312,6 +24628,22 @@ version toolchain ========= =============================== +.. _list_software_pretty-yaml_1160: + +*pretty-yaml* ++++++++++++++ + +PyYAML-based python module to produce pretty and readable YAML-serialized data. This module is for serialization only, see ruamel.yaml module for literate YAML parsing (keeping track of comments, spacing, line/column numbers of values, etc). + +*homepage*: https://github.com/mk-fg/pretty-yaml + +=========== ================= +version toolchain +=========== ================= +``19.12.0`` ``GCCcore/8.3.0`` +=========== ================= + + .. _list_software_Primer3_674: *Primer3* @@ -23589,6 +24921,22 @@ version versionsuffix toolchain ========= ================== ================================== +.. _list_software_PRSice_550: + +*PRSice* +++++++++ + +PRSice (pronounced 'precise') is a Polygenic Risk Score software for calculating, applying, evaluating and plotting the results of polygenic risk scores (PRS) analyses. + +*homepage*: https://www.prsice.info/ + +========== ================= +version toolchain +========== ================= +``2.2.12`` ``GCCcore/8.3.0`` +========== ================= + + .. _list_software_pscom_546: *pscom* @@ -23988,7 +25336,7 @@ version versionsuffix toolchain Python bindings for the cairo library -*homepage*: https://cairographics.org/pycairo/ +*homepage*: https://pycairo.readthedocs.io/ ========== ================== ================= version versionsuffix toolchain @@ -24000,6 +25348,7 @@ version versionsuffix toolchain ``1.18.0`` ``-Python-2.7.15`` ``foss/2018b`` ``1.18.0`` ``-Python-3.6.6`` ``foss/2018b`` ``1.18.0`` ``-Python-3.7.2`` ``GCCcore/8.2.0`` +``1.18.2`` ``GCCcore/8.3.0`` ========== ================== ================= @@ -24036,6 +25385,22 @@ version toolchain ========= =============== +.. _list_software_pycodestyle_1205: + +*pycodestyle* ++++++++++++++ + +pycodestyle is a tool to check your Python code against some of the style conventions in PEP 8. + +*homepage*: https://pycodestyle.readthedocs.io + +========= ================= =============== +version versionsuffix toolchain +========= ================= =============== +``2.5.0`` ``-Python-3.6.4`` ``intel/2018a`` +========= ================= =============== + + .. _list_software_PyCogent_809: *PyCogent* @@ -24102,6 +25467,7 @@ version versionsuffix toolchain ========= ================== ================= ``0.9.9`` ``-Python-2.7.11`` ``intel/2016a`` ``1.2.2`` ``GCCcore/8.2.0`` +``1.4.2`` ``GCCcore/8.3.0`` ========= ================== ================= @@ -24122,6 +25488,22 @@ version versionsuffix toolchain ============ ================== =============== +.. _list_software_pydot_560: + +*pydot* ++++++++ + +Python interface to Graphviz's Dot language. + +*homepage*: https://github.com/pydot/pydot + +========= ============== +version toolchain +========= ============== +``1.4.1`` ``foss/2019b`` +========= ============== + + .. _list_software_pyEGA3_489: *pyEGA3* @@ -24180,11 +25562,12 @@ A pythonic wrapper around FFTW, the FFT library, presenting a unified interface *homepage*: https://github.com/pyFFTW/pyFFTW -========== =============== -version toolchain -========== =============== -``0.11.1`` ``intel/2019a`` -========== =============== +========== ================= =============== +version versionsuffix toolchain +========== ================= =============== +``0.11.1`` ``intel/2019a`` +``0.11.1`` ``-Python-3.6.6`` ``foss/2018b`` +========== ================= =============== .. _list_software_pyfits_671: @@ -24291,9 +25674,9 @@ version versionsuffix toolchain *PyGObject* +++++++++++ -Python Bindings for GLib/GObject/GIO/GTK+ +PyGObject is a Python package which provides bindings for GObject based libraries such as GTK, GStreamer, WebKitGTK, GLib, GIO and many more. -*homepage*: http://www.pygtk.org/ +*homepage*: https://pygobject.readthedocs.io/ ========== ================== ================= version versionsuffix toolchain @@ -24302,10 +25685,28 @@ version versionsuffix toolchain ``2.28.6`` ``-Python-2.7.14`` ``intel/2017b`` ``2.28.7`` ``-Python-2.7.14`` ``intel/2018a`` ``2.28.7`` ``-Python-2.7.15`` ``foss/2018b`` +``3.34.0`` ``-Python-2.7.16`` ``GCCcore/8.3.0`` ``3.34.0`` ``-Python-3.7.2`` ``GCCcore/8.2.0`` +``3.34.0`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` ========== ================== ================= +.. _list_software_pygraphviz_1108: + +*pygraphviz* +++++++++++++ + +PyGraphviz is a Python interface to the Graphviz graph layout and visualization package. With PyGraphviz you can create, edit, read, write, and draw graphs using Python to access the Graphviz graph data structure and layout algorithms. + +*homepage*: https://pygraphviz.github.io/ + +======= ============== +version toolchain +======= ============== +``1.5`` ``foss/2019b`` +======= ============== + + .. _list_software_pygrib_653: *pygrib* @@ -24427,6 +25828,22 @@ version versionsuffix toolchain ========= ================= =============== +.. _list_software_pylift_664: + +*pylift* +++++++++ + +pylift is an uplift library that provides, primarily: (1) Fast uplift modeling implementations and (2) Evaluation tools (UpliftEval class). + +*homepage*: https://github.com/df-foundation/pylift + +========= ================= ============== +version versionsuffix toolchain +========= ================= ============== +``0.1.5`` ``-Python-3.7.4`` ``foss/2019b`` +========= ================= ============== + + .. _list_software_Pylint_640: *Pylint* @@ -24496,6 +25913,22 @@ version versionsuffix toolchain ========= ================= =============== +.. _list_software_PyMC3_396: + +*PyMC3* ++++++++ + +Probabilistic Programming in Python: Bayesian Modeling and Probabilistic Machine Learning with Theano + +*homepage*: https://docs.pymc.io/ + +======= ================= =============== +version versionsuffix toolchain +======= ================= =============== +``3.8`` ``-Python-3.7.4`` ``intel/2019b`` +======= ================= =============== + + .. _list_software_pymemcache_1052: *pymemcache* @@ -24567,6 +26000,22 @@ version versionsuffix toolchain =========== ================== =============================== +.. _list_software_pyparsing_989: + +*pyparsing* ++++++++++++ + +The pyparsing module is an alternative approach to creating and executing simple grammars, vs. the traditional lex/yacc approach, or the use of regular expressions. The pyparsing module provides a library of classes that client code uses to construct the grammar directly in Python code. + +*homepage*: https://github.com/pyparsing/pyparsing + +========= ================== ================= +version versionsuffix toolchain +========= ================== ================= +``2.4.6`` ``-Python-2.7.16`` ``GCCcore/8.3.0`` +========= ================== ================= + + .. _list_software_pyplusplus_1137: *pyplusplus* @@ -24593,11 +26042,12 @@ Python interface to PROJ4 library for cartographic transformations *homepage*: https://pyproj4.github.io/pyproj -========= ================= -version toolchain -========= ================= -``2.1.3`` ``GCCcore/8.2.0`` -========= ================= +========= ================= ================= +version versionsuffix toolchain +========= ================= ================= +``2.1.3`` ``GCCcore/8.2.0`` +``2.4.2`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` +========= ================= ================= .. _list_software_pyqstem_787: @@ -24654,7 +26104,7 @@ version versionsuffix toolchain ``5.8.2`` ``-Python-2.7.13`` ``intel/2017a`` ``5.9.2`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` ``5.9.2`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` -``5.11.3`` ``-Python-3.6.6`` ``foss/2018b`` +``5.11.3`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` ``5.12.1`` ``-Python-2.7.15`` ``GCCcore/8.2.0`` ``5.12.1`` ``-Python-3.7.2`` ``GCCcore/8.2.0`` ========== ================== =============================== @@ -24669,12 +26119,29 @@ PyQtGraph is a pure-python graphics and GUI library built on PyQt4/PySide and nu *homepage*: http://www.pyqtgraph.org/ -========== ================= =============== -version versionsuffix toolchain -========== ================= =============== -``0.10.0`` ``-Python-3.6.4`` ``intel/2018a`` -``0.10.0`` ``-Python-3.7.2`` ``intel/2019a`` -========== ================= =============== +========== ================= =============================== +version versionsuffix toolchain +========== ================= =============================== +``0.10.0`` ``-Python-3.6.4`` ``intel/2018a`` +``0.10.0`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` +``0.10.0`` ``-Python-3.7.2`` ``intel/2019a`` +========== ================= =============================== + + +.. _list_software_PyRe_384: + +*PyRe* +++++++ + +PyRe (Python Reliability) is a Python module for structural reliability analysis. + +*homepage*: https://hackl.science/pyre + +================== ================= =============================== +version versionsuffix toolchain +================== ================= =============================== +``5.0.3-20190221`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` +================== ================= =============================== .. _list_software_PyRETIS_592: @@ -24879,7 +26346,7 @@ version versionsuffix toolchain PyTables is a package for managing hierarchical datasets and designed to efficiently and easily cope with extremely large amounts of data. PyTables is built on top of the HDF5 library, using the Python language and the NumPy package. It features an object-oriented interface that, combined with C extensions for the performance-critical parts of the code (generated using Cython), makes it a fast, yet extremely easy to use tool for interactively browse, process and search very large amounts of data. One important feature of PyTables is that it optimizes memory and disk resources so that data takes much less space (specially if on-flight compression is used) than other solutions such as relational or object oriented databases. -*homepage*: http://www.pytables.org +*homepage*: https://www.pytables.org =========== ================== ================================== version versionsuffix toolchain @@ -24897,6 +26364,8 @@ version versionsuffix toolchain ``3.4.4`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b`` ``3.5.2`` ``intel/2019a`` ``3.5.2`` ``-Python-2.7.14`` ``intel/2018a`` +``3.5.2`` ``-Python-2.7.16`` ``intel/2019b`` +``3.6.1`` ``-Python-3.7.4`` ``foss/2019b`` =========== ================== ================================== @@ -24989,13 +26458,14 @@ version versionsuffix toolchain Python interface to the igraph high performance graph library, primarily aimed at complex network research and analysis. -*homepage*: http://igraph.org/python +*homepage*: https://igraph.org/python =============== ================== =============== version versionsuffix toolchain =============== ================== =============== ``0.7.1.post6`` ``-Python-2.7.14`` ``intel/2017b`` ``0.7.1.post6`` ``-Python-3.6.6`` ``foss/2018b`` +``0.8.0`` ``foss/2019b`` =============== ================== =============== @@ -25020,18 +26490,35 @@ version versionsuffix toolchain *python-parasail* +++++++++++++++++ -This package contains Python bindings for parasail. +Python Bindings for the Parasail C Library -*homepage*: https://pypi.org/project/parasail/ +*homepage*: https://github.com/jeffdaily/parasail-python ========== ================== =============== version versionsuffix toolchain ========== ================== =============== ``1.1.12`` ``-Python-2.7.14`` ``intel/2018a`` ``1.1.16`` ``-Python-3.6.6`` ``foss/2018b`` +``1.2`` ``-Python-3.7.4`` ``intel/2019b`` ========== ================== =============== +.. _list_software_python-weka-wrapper3_2008: + +*python-weka-wrapper3* +++++++++++++++++++++++ + +Python3 wrapper for the Weka Machine Learning Workbench + +*homepage*: https://github.com/fracpete/python-weka-wrapper3 + +========== ================= ============== +version versionsuffix toolchain +========== ================= ============== +``0.1.11`` ``-Python-3.7.4`` ``foss/2019b`` +========== ================= ============== + + .. _list_software_pythran_774: *pythran* @@ -25069,9 +26556,27 @@ version versionsuffix toolchain ``1.1.0`` ``-Python-3.7.2`` ``foss/2019a`` ``1.2.0`` ``-Python-3.7.2`` ``foss/2019a``, ``fosscuda/2019a`` ``1.3.1`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` +``1.4.0`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` ========= ============================= ================================== +.. _list_software_PyTorch-Geometric_1685: + +*PyTorch-Geometric* ++++++++++++++++++++ + +PyTorch Geometric (PyG) is a geometric deep learning extension library for PyTorch. + +*homepage*: https://github.com/rusty1s/pytorch_geometric + +========= =============================== ============== +version versionsuffix toolchain +========= =============================== ============== +``1.3.2`` ``-Python-3.7.4`` ``foss/2019b`` +``1.4.2`` ``-Python-3.7.4-PyTorch-1.4.0`` ``foss/2019b`` +========= =============================== ============== + + .. _list_software_PyYAML_508: *PyYAML* @@ -25134,7 +26639,7 @@ version versionsuffix toolchain --- -:ref:`list_software_Q6_135` - :ref:`list_software_QCA_213` - :ref:`list_software_qcint_543` - :ref:`list_software_QDD_217` - :ref:`list_software_QEMU_312` - :ref:`list_software_QGIS_308` - :ref:`list_software_Qhull_518` - :ref:`list_software_QIIME_373` - :ref:`list_software_QIIME2_423` - :ref:`list_software_Qiskit_629` - :ref:`list_software_QJson_491` - :ref:`list_software_QML_234` - :ref:`list_software_qpth_445` - :ref:`list_software_qrupdate_870` - :ref:`list_software_QScintilla_1012` - :ref:`list_software_Qt_197` - :ref:`list_software_Qt5_250` - :ref:`list_software_Qt5Webkit_864` - :ref:`list_software_QtKeychain_1009` - :ref:`list_software_QTLtools_802` - :ref:`list_software_qtop_452` - :ref:`list_software_Qualimap_826` - :ref:`list_software_Quandl_613` - :ref:`list_software_QuantumESPRESSO_1375` - :ref:`list_software_QUAST_398` - :ref:`list_software_QuaZIP_538` - :ref:`list_software_QuickFF_649` - :ref:`list_software_Quip_415` - :ref:`list_software_Quorum_649` - :ref:`list_software_QuTiP_467` - :ref:`list_software_Qwt_316` - :ref:`list_software_QwtPolar_826` +:ref:`list_software_Q6_135` - :ref:`list_software_QCA_213` - :ref:`list_software_qcat_425` - :ref:`list_software_qcint_543` - :ref:`list_software_QDD_217` - :ref:`list_software_QEMU_312` - :ref:`list_software_QGIS_308` - :ref:`list_software_Qhull_518` - :ref:`list_software_QIIME_373` - :ref:`list_software_QIIME2_423` - :ref:`list_software_Qiskit_629` - :ref:`list_software_QJson_491` - :ref:`list_software_QML_234` - :ref:`list_software_qpth_445` - :ref:`list_software_qrupdate_870` - :ref:`list_software_QScintilla_1012` - :ref:`list_software_Qt_197` - :ref:`list_software_Qt5_250` - :ref:`list_software_Qt5Webkit_864` - :ref:`list_software_QtKeychain_1009` - :ref:`list_software_QTLtools_802` - :ref:`list_software_qtop_452` - :ref:`list_software_Qualimap_826` - :ref:`list_software_Quandl_613` - :ref:`list_software_QuantumESPRESSO_1375` - :ref:`list_software_QUAST_398` - :ref:`list_software_QuaZIP_538` - :ref:`list_software_QuickFF_649` - :ref:`list_software_Quip_415` - :ref:`list_software_Quorum_649` - :ref:`list_software_QuTiP_467` - :ref:`list_software_Qwt_316` - :ref:`list_software_QwtPolar_826` .. _list_software_Q6_135: @@ -25170,6 +26675,22 @@ version toolchain ========= ================================================== +.. _list_software_qcat_425: + +*qcat* +++++++ + +qcat is a Python command-line tool for demultiplexing Oxford Nanopore reads from FASTQ files + +*homepage*: https://github.com/nanoporetech/qcat/releases + +========= ================= =============== +version versionsuffix toolchain +========= ================= =============== +``1.1.0`` ``-Python-3.7.4`` ``intel/2019b`` +========= ================= =============== + + .. _list_software_qcint_543: *qcint* @@ -25241,7 +26762,7 @@ version versionsuffix toolchain *Qhull* +++++++ -Qhull computes the convex hull, Delaunay triangulation, Voronoi diagram, halfspace intersection about a point, furthest-site Delaunay triangulation, and furthest-site Voronoi diagram. The source code runs in 2-d, 3-d, 4-d, and higher dimensions. Qhull implements the Quickhull algorithm for computing the convex hull. +Qhull computes the convex hull, Delaunay triangulation, Voronoi diagram, halfspace intersection about a point, furthest-site Delaunay triangulation, and furthest-site Voronoi diagram. The source code runs in 2-d, 3-d, 4-d, and higher dimensions. Qhull implements the Quickhull algorithm for computing the convex hull. *homepage*: http://www.qhull.org @@ -25249,6 +26770,7 @@ Qhull computes the convex hull, Delaunay triangulation, Voronoi diagram, halfspa version toolchain ========== ============================================================================================================================================================================= ``2015.2`` ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2017b``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a`` +``2019.1`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` ========== ============================================================================================================================================================================= @@ -25361,11 +26883,11 @@ qrupdate is a Fortran library for fast updates of QR and Cholesky decompositions *homepage*: https://sourceforge.net/projects/qrupdate/ -========= ======================================================================================================================================== -version toolchain -========= ======================================================================================================================================== -``1.1.2`` ``GCC/5.4.0-2.26``, ``GCCcore/6.4.0``, ``foss/2016a``, ``foss/2018a``, ``foss/2018b``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a`` -========= ======================================================================================================================================== +========= ================================================================================================================================================================================= +version toolchain +========= ================================================================================================================================================================================= +``1.1.2`` ``GCC/5.4.0-2.26``, ``GCC/8.2.0-2.31.1``, ``GCCcore/6.4.0``, ``GCCcore/8.3.0``, ``foss/2016a``, ``foss/2018a``, ``foss/2018b``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a`` +========= ================================================================================================================================================================================= .. _list_software_QScintilla_1012: @@ -25414,20 +26936,20 @@ Qt is a comprehensive cross-platform C++ application framework. *homepage*: http://qt.io/ -========== ================================================================================= -version toolchain -========== ================================================================================= -``5.6.0`` ``foss/2016a``, ``intel/2016a`` -``5.7.0`` ``foss/2016a``, ``foss/2016b``, ``intel/2016a``, ``intel/2016b`` -``5.7.1`` ``intel/2016b`` -``5.8.0`` ``foss/2017a``, ``foss/2017b``, ``intel/2016b``, ``intel/2017a``, ``intel/2017b`` -``5.9.3`` ``foss/2017b`` -``5.9.8`` ``fosscuda/2018b`` -``5.10.1`` ``foss/2018a``, ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018a`` -``5.11.2`` ``foss/2018b`` -``5.12.3`` ``GCCcore/8.2.0`` -``5.13.1`` ``GCCcore/8.3.0`` -========== ================================================================================= +========== ==================================================================================== +version toolchain +========== ==================================================================================== +``5.6.0`` ``foss/2016a``, ``intel/2016a`` +``5.7.0`` ``foss/2016a``, ``foss/2016b``, ``intel/2016a``, ``intel/2016b`` +``5.7.1`` ``intel/2016b`` +``5.8.0`` ``foss/2017a``, ``foss/2017b``, ``intel/2016b``, ``intel/2017a``, ``intel/2017b`` +``5.9.3`` ``foss/2017b`` +``5.9.8`` ``fosscuda/2018b`` +``5.10.1`` ``foss/2018a``, ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018a``, ``intel/2018b`` +``5.11.2`` ``foss/2018b`` +``5.12.3`` ``GCCcore/8.2.0`` +``5.13.1`` ``GCCcore/8.3.0`` +========== ==================================================================================== .. _list_software_Qt5Webkit_864: @@ -25548,6 +27070,7 @@ version versionsuffix toolchain ``6.2.1`` ``iomkl/2017b`` ``6.3`` ``foss/2018b``, ``intel/2018b`` ``6.4.1`` ``intel/2019a`` +``6.5`` ``intel/2019a`` ========= ============= =============================== @@ -25693,7 +27216,7 @@ version toolchain --- -:ref:`list_software_R_82` - :ref:`list_software_R-bundle-Bioconductor_2065` - :ref:`list_software_R-keras_661` - :ref:`list_software_R-tesseract_1101` - :ref:`list_software_Racon_499` - :ref:`list_software_Ragout_626` - :ref:`list_software_randfold_842` - :ref:`list_software_randrproto_1099` - :ref:`list_software_RapidJSON_810` - :ref:`list_software_rapidtide_950` - :ref:`list_software_Rascaf_592` - :ref:`list_software_RASPA2_425` - :ref:`list_software_RAxML_420` - :ref:`list_software_RBFOpt_525` - :ref:`list_software_Rcorrector_1061` - :ref:`list_software_rCUDA_399` - :ref:`list_software_RDFlib_531` - :ref:`list_software_RDKit_446` - :ref:`list_software_RDP-Classifier_1304` - :ref:`list_software_re2c_364` - :ref:`list_software_Reads2snp_882` - :ref:`list_software_Redundans_932` - :ref:`list_software_ReFrame_674` - :ref:`list_software_RELION_457` - :ref:`list_software_REMORA_454` - :ref:`list_software_renderproto_1204` - :ref:`list_software_RepastHPC_842` - :ref:`list_software_RepeatMasker_1220` - :ref:`list_software_requests_892` - :ref:`list_software_RERconverge_1090` - :ref:`list_software_rgdal_522` - :ref:`list_software_rgeos_544` - :ref:`list_software_rhdf5_473` - :ref:`list_software_rioxarray_993` - :ref:`list_software_rjags_535` - :ref:`list_software_Rmath_508` - :ref:`list_software_RMBlast_661` - :ref:`list_software_RNA-SeQC_602` - :ref:`list_software_RNAclust_780` - :ref:`list_software_RNAcode_636` - :ref:`list_software_RNAIndel_717` - :ref:`list_software_rnaQUAST_719` - :ref:`list_software_RNAz_347` - :ref:`list_software_Roary_525` - :ref:`list_software_ROI_PAC_541` - :ref:`list_software_ROME_307` - :ref:`list_software_ROOT_324` - :ref:`list_software_rootpy_685` - :ref:`list_software_Rosetta_738` - :ref:`list_software_rpmrebuild_1078` - :ref:`list_software_rpy2_397` - :ref:`list_software_RQGIS3_441` - :ref:`list_software_RSEM_311` - :ref:`list_software_RSeQC_414` - :ref:`list_software_RStan_488` - :ref:`list_software_RTG-Tools_811` - :ref:`list_software_Rtree_514` - :ref:`list_software_Ruby_418` - :ref:`list_software_Rust_430` +:ref:`list_software_R_82` - :ref:`list_software_R-bundle-Bioconductor_2065` - :ref:`list_software_R-keras_661` - :ref:`list_software_R-tesseract_1101` - :ref:`list_software_Racon_499` - :ref:`list_software_Ragout_626` - :ref:`list_software_randfold_842` - :ref:`list_software_randrproto_1099` - :ref:`list_software_RapidJSON_810` - :ref:`list_software_rapidtide_950` - :ref:`list_software_Rascaf_592` - :ref:`list_software_RASPA2_425` - :ref:`list_software_RAxML_420` - :ref:`list_software_RAxML-NG_614` - :ref:`list_software_Ray_300` - :ref:`list_software_RBFOpt_525` - :ref:`list_software_rclone_643` - :ref:`list_software_Rcorrector_1061` - :ref:`list_software_rCUDA_399` - :ref:`list_software_RDFlib_531` - :ref:`list_software_RDKit_446` - :ref:`list_software_RDP-Classifier_1304` - :ref:`list_software_re2c_364` - :ref:`list_software_Reads2snp_882` - :ref:`list_software_Red_283` - :ref:`list_software_Redundans_932` - :ref:`list_software_ReFrame_674` - :ref:`list_software_RELION_457` - :ref:`list_software_REMORA_454` - :ref:`list_software_renderproto_1204` - :ref:`list_software_RepastHPC_842` - :ref:`list_software_RepeatMasker_1220` - :ref:`list_software_requests_892` - :ref:`list_software_RERconverge_1090` - :ref:`list_software_rgdal_522` - :ref:`list_software_rgeos_544` - :ref:`list_software_rhdf5_473` - :ref:`list_software_rioxarray_993` - :ref:`list_software_rjags_535` - :ref:`list_software_Rmath_508` - :ref:`list_software_RMBlast_661` - :ref:`list_software_RNA-SeQC_602` - :ref:`list_software_RNAclust_780` - :ref:`list_software_RNAcode_636` - :ref:`list_software_RNAIndel_717` - :ref:`list_software_rnaQUAST_719` - :ref:`list_software_RNAz_347` - :ref:`list_software_Roary_525` - :ref:`list_software_ROI_PAC_541` - :ref:`list_software_ROME_307` - :ref:`list_software_ROOT_324` - :ref:`list_software_rootpy_685` - :ref:`list_software_Rosetta_738` - :ref:`list_software_rpmrebuild_1078` - :ref:`list_software_rpy2_397` - :ref:`list_software_RQGIS3_441` - :ref:`list_software_RSEM_311` - :ref:`list_software_RSeQC_414` - :ref:`list_software_RStan_488` - :ref:`list_software_rstanarm_872` - :ref:`list_software_RTG-Tools_811` - :ref:`list_software_Rtree_514` - :ref:`list_software_Ruby_418` - :ref:`list_software_Rust_430` .. _list_software_R_82: @@ -25735,19 +27258,20 @@ Bioconductor provides tools for the analysis and coprehension of high-throughpu *homepage*: https://bioconductor.org -======= ============= =============================== -version versionsuffix toolchain -======= ============= =============================== -``3.2`` ``-R-3.2.3`` ``foss/2016a``, ``intel/2016a`` -``3.3`` ``-R-3.3.1`` ``intel/2016b`` -``3.5`` ``-R-3.4.0`` ``intel/2017a`` -``3.6`` ``-R-3.4.3`` ``foss/2017b``, ``intel/2017b`` -``3.6`` ``-R-3.4.4`` ``intel/2018a`` -``3.7`` ``-R-3.5.0`` ``iomkl/2018a`` -``3.7`` ``-R-3.5.1`` ``foss/2018b`` -``3.8`` ``-R-3.5.1`` ``foss/2018b`` -``3.9`` ``-R-3.6.0`` ``foss/2019a`` -======= ============= =============================== +======== ============= =============================== +version versionsuffix toolchain +======== ============= =============================== +``3.2`` ``-R-3.2.3`` ``foss/2016a``, ``intel/2016a`` +``3.3`` ``-R-3.3.1`` ``intel/2016b`` +``3.5`` ``-R-3.4.0`` ``intel/2017a`` +``3.6`` ``-R-3.4.3`` ``foss/2017b``, ``intel/2017b`` +``3.6`` ``-R-3.4.4`` ``intel/2018a`` +``3.7`` ``-R-3.5.0`` ``iomkl/2018a`` +``3.7`` ``-R-3.5.1`` ``foss/2018b`` +``3.8`` ``-R-3.5.1`` ``foss/2018b`` +``3.9`` ``-R-3.6.0`` ``foss/2019a`` +``3.10`` ``foss/2019b`` +======== ============= =============================== .. _list_software_R-keras_661: @@ -25764,6 +27288,7 @@ version versionsuffix toolchain =========== ========================= ================================== ``2.1.6`` ``-R-3.4.4`` ``foss/2018a`` ``2.2.5.0`` ``-Python-3.7.2-R-3.6.0`` ``foss/2019a``, ``fosscuda/2019a`` +``2.2.5.0`` ``-Python-3.7.4-R-3.6.2`` ``foss/2019b``, ``fosscuda/2019b`` =========== ========================= ================================== @@ -25788,16 +27313,17 @@ version versionsuffix toolchain *Racon* +++++++ -Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads. +Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads -*homepage*: https://github.com/lbcb-sci/racon +*homepage*: https://github.com/clara-genomics/racon-gpu -========= ================= -version toolchain -========= ================= -``1.3.2`` ``GCCcore/8.2.0`` -``1.4.7`` ``GCCcore/8.2.0`` -========= ================= +========== ==================================== +version toolchain +========== ==================================== +``1.3.2`` ``GCCcore/8.2.0`` +``1.4.7`` ``GCCcore/8.2.0``, ``gcccuda/2019b`` +``1.4.10`` ``GCC/7.3.0-2.30`` +========== ==================================== .. _list_software_Ragout_626: @@ -25857,11 +27383,11 @@ A fast JSON parser/generator for C++ with both SAX/DOM style API *homepage*: https://rapidjson.org -========= ================= -version toolchain -========= ================= -``1.1.0`` ``GCCcore/8.2.0`` -========= ================= +========= ==================================== +version toolchain +========= ==================================== +``1.1.0`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` +========= ==================================== .. _list_software_rapidtide_950: @@ -25930,10 +27456,42 @@ version versionsuffix toolchain ``8.2.11`` ``-hybrid-avx`` ``foss/2017b``, ``intel/2017b`` ``8.2.11`` ``-hybrid-avx2`` ``foss/2017b``, ``intel/2017b``, ``intel/2018a`` ``8.2.11`` ``-hybrid-sse3`` ``foss/2017b``, ``intel/2017b`` -``8.2.12`` ``-hybrid-avx2`` ``intel/2019a`` +``8.2.12`` ``-hybrid-avx2`` ``iimpi/2019b``, ``intel/2019a`` ========== ================ ================================================ +.. _list_software_RAxML-NG_614: + +*RAxML-NG* +++++++++++ + +RAxML-NG is a phylogenetic tree inference tool which uses maximum-likelihood (ML) optimality criterion. Its search heuristic is based on iteratively performing a series of Subtree Pruning and Regrafting (SPR) moves, which allows to quickly navigate to the best-known ML tree. + +*homepage*: https://github.com/amkozlov/raxml-ng + +========= =============== +version toolchain +========= =============== +``0.9.0`` ``gompi/2019b`` +========= =============== + + +.. _list_software_Ray_300: + +*Ray* ++++++ + +Parallel genome assemblies for parallel DNA sequencing + +*homepage*: http://denovoassembler.sourceforge.net/ + +========= =============== +version toolchain +========= =============== +``2.3.1`` ``iimpi/2019a`` +========= =============== + + .. _list_software_RBFOpt_525: *RBFOpt* @@ -25951,6 +27509,22 @@ version versionsuffix toolchain ========= ================= =============== +.. _list_software_rclone_643: + +*rclone* +++++++++ + +Rclone is a command line program to sync files and directories to and from a variety of online storage services + +*homepage*: https://rclone.org/ + +======== ============= ========== +version versionsuffix toolchain +======== ============= ========== +``1.42`` ``-amd64`` ``system`` +======== ============= ========== + + .. _list_software_Rcorrector_1061: *Rcorrector* @@ -25993,11 +27567,11 @@ RDFLib is a Python library for working with RDF, a simple yet powerful language *homepage*: https://github.com/RDFLib/rdflib -========= ============== -version toolchain -========= ============== -``4.2.2`` ``foss/2019a`` -========= ============== +========= ================================= +version toolchain +========= ================================= +``4.2.2`` ``GCCcore/8.3.0``, ``foss/2019a`` +========= ================================= .. _list_software_RDKit_446: @@ -26013,6 +27587,7 @@ RDKit is a collection of cheminformatics and machine-learning software written i version versionsuffix toolchain ============= ================= =============== ``2018.09.3`` ``-Python-3.6.6`` ``intel/2018b`` +``2019.09.3`` ``-Python-3.7.4`` ``foss/2019b`` ============= ================= =============== @@ -26066,6 +27641,22 @@ version toolchain ======= ========== +.. _list_software_Red_283: + +*Red* ++++++ + +Red (REpeat Detector) + +*homepage*: http://toolsmith.ens.utulsa.edu/ + +============== ======================================== +version toolchain +============== ======================================== +``2015-05-22`` ``iccifort/2019.1.144-GCC-8.2.0-2.31.1`` +============== ======================================== + + .. _list_software_Redundans_932: *Redundans* @@ -26097,6 +27688,7 @@ version toolchain ``2.18`` ``system`` ``2.19`` ``system`` ``2.20`` ``system`` +``2.21`` ``system`` ======== ========== @@ -26238,6 +27830,7 @@ Provides bindings to the 'Geospatial' Data Abstraction Library ('GDAL') (>= 1.11 version versionsuffix toolchain ========= ============= ============== ``1.4-4`` ``-R-3.6.0`` ``foss/2019a`` +``1.4-8`` ``-R-3.6.2`` ``foss/2019b`` ========= ============= ============== @@ -26255,6 +27848,7 @@ version versionsuffix toolchain ========== ============= =============== ``0.3-17`` ``-R-3.2.3`` ``intel/2016a`` ``0.5-1`` ``-R-3.6.0`` ``foss/2019a`` +``0.5-2`` ``-R-3.6.2`` ``foss/2019b`` ========== ============= =============== @@ -26298,7 +27892,7 @@ version versionsuffix toolchain The rjags package is an interface to the JAGS library. -*homepage*: http://cran.r-project.org/web/packages/rjags +*homepage*: https://cran.r-project.org/web/packages/rjags ======= ============= =============== version versionsuffix toolchain @@ -26306,6 +27900,7 @@ version versionsuffix toolchain ``4-6`` ``-R-3.4.0`` ``intel/2017a`` ``4-6`` ``-R-3.4.3`` ``intel/2017b`` ``4-8`` ``-R-3.5.1`` ``foss/2018b`` +``4-9`` ``-R-3.6.0`` ``foss/2019a`` ======= ============= =============== @@ -26505,6 +28100,7 @@ version versionsuffix toolchain ``6.10.04`` ``-Python-2.7.13`` ``intel/2017a`` ``6.10.08`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` ``6.14.06`` ``-Python-2.7.15`` ``foss/2018b`` +``6.14.06`` ``-Python-3.6.6`` ``foss/2018b`` ``v5.34.34`` ``-Python-2.7.11`` ``intel/2016a`` ``v5.34.36`` ``-Python-2.7.11`` ``intel/2016a`` ``v6.06.02`` ``-Python-2.7.12`` ``intel/2016b`` @@ -26567,15 +28163,16 @@ version toolchain *rpy2* ++++++ -rpy2 is a redesign and rewrite of rpy. It is providing a low-level interface to R from Python, a proposed high-level interface, including wrappers to graphical libraries, as well as R-like structures and functions. +rpy2 is an interface to R running embedded in a Python process. -*homepage*: http://rpy.sourceforge.net/ +*homepage*: https://rpy2.bitbucket.io/ ========= ================== =============== version versionsuffix toolchain ========= ================== =============== ``2.7.9`` ``-Python-2.7.12`` ``foss/2016b`` ``2.8.2`` ``-Python-2.7.13`` ``intel/2017a`` +``3.2.6`` ``-Python-3.7.4`` ``foss/2019b`` ========= ================== =============== @@ -26650,6 +28247,22 @@ version versionsuffix toolchain ========== ============= =============================== +.. _list_software_rstanarm_872: + +*rstanarm* +++++++++++ + +Estimates previously compiled regression models using the 'rstan' package, which provides the R interface to the Stan C++ library for Bayesian estimation. + +*homepage*: https://r-forge.r-project.org/projects/rstanarm + +========== ============= ============== +version versionsuffix toolchain +========== ============= ============== +``2.19.3`` ``-R-3.6.2`` ``foss/2019b`` +========== ============= ============== + + .. _list_software_RTG-Tools_811: *RTG-Tools* @@ -26687,7 +28300,7 @@ version versionsuffix toolchain *Ruby* ++++++ -Ruby is a dynamic, open source programming language with a focus on simplicity and productivity. It has an elegant syntax that is natural to read and easy to write. +Ruby is a dynamic, open source programming language with a focus on simplicity and productivity. It has an elegant syntax that is natural to read and easy to write. *homepage*: https://www.ruby-lang.org @@ -26703,6 +28316,7 @@ version toolchain ``2.5.1`` ``intel/2018a`` ``2.6.1`` ``GCCcore/7.3.0`` ``2.6.3`` ``GCCcore/8.2.0`` +``2.7.1`` ``GCCcore/8.3.0`` ========= ================================================ @@ -26737,7 +28351,7 @@ version toolchain --- -:ref:`list_software_S-Lang_514` - :ref:`list_software_S4_135` - :ref:`list_software_SAGE_288` - :ref:`list_software_Sailfish_819` - :ref:`list_software_SALib_427` - :ref:`list_software_Salmon_618` - :ref:`list_software_SALMON-TDDFT_877` - :ref:`list_software_Sambamba_788` - :ref:`list_software_Samcef_591` - :ref:`list_software_samclip_745` - :ref:`list_software_SAMtools_786` - :ref:`list_software_SAS_231` - :ref:`list_software_savvy_569` - :ref:`list_software_Saxon-HE_707` - :ref:`list_software_sbt_329` - :ref:`list_software_ScaLAPACK_707` - :ref:`list_software_Scalasca_795` - :ref:`list_software_SCALCE_427` - :ref:`list_software_sciClone_816` - :ref:`list_software_ScientificPython_1667` - :ref:`list_software_scikit-allel_1214` - :ref:`list_software_scikit-image_1207` - :ref:`list_software_scikit-learn_1222` - :ref:`list_software_scikit-multilearn_1777` - :ref:`list_software_scikit-optimize_1573` - :ref:`list_software_SCIPhI_480` - :ref:`list_software_scipy_552` - :ref:`list_software_SciPy-bundle_1167` - :ref:`list_software_SCnorm_594` - :ref:`list_software_Scoary_625` - :ref:`list_software_SCons_486` - :ref:`list_software_SCOOP_388` - :ref:`list_software_Score-P_633` - :ref:`list_software_SCOTCH_452` - :ref:`list_software_scp_326` - :ref:`list_software_Scrappie_823` - :ref:`list_software_SDCC_285` - :ref:`list_software_SDL2_277` - :ref:`list_software_Seaborn_714` - :ref:`list_software_SearchGUI_827` - :ref:`list_software_segemehl_842` - :ref:`list_software_SelEstim_806` - :ref:`list_software_sep_328` - :ref:`list_software_Seq-Gen_624` - :ref:`list_software_seq2HLA_592` - :ref:`list_software_SeqAn_472` - :ref:`list_software_SeqAn3_523` - :ref:`list_software_Seqmagick_917` - :ref:`list_software_SeqPrep_704` - :ref:`list_software_seqtk_552` - :ref:`list_software_Serf_400` - :ref:`list_software_setuptools_1122` - :ref:`list_software_Seurat_628` - :ref:`list_software_Shannon_725` - :ref:`list_software_shapAAR_640` - :ref:`list_software_SHAPEIT_526` - :ref:`list_software_sharutils_991` - :ref:`list_software_shift_542` - :ref:`list_software_SHORE_385` - :ref:`list_software_Short-Pair_969` - :ref:`list_software_shovill_769` - :ref:`list_software_shrinkwrap_1097` - :ref:`list_software_Sibelia_697` - :ref:`list_software_sickle_635` - :ref:`list_software_Siesta_617` - :ref:`list_software_SimPEG_517` - :ref:`list_software_SIMPLE_458` - :ref:`list_software_SimpleElastix_1348` - :ref:`list_software_SimpleITK_850` - :ref:`list_software_simpy_562` - :ref:`list_software_SimVascular_1130` - :ref:`list_software_SingleM_687` - :ref:`list_software_Singularity_1179` - :ref:`list_software_SIONlib_624` - :ref:`list_software_SIP_236` - :ref:`list_software_SKESA_375` - :ref:`list_software_sketchmap_960` - :ref:`list_software_skewer_657` - :ref:`list_software_SLEPc_407` - :ref:`list_software_slepc4py_820` - :ref:`list_software_sleuth_661` - :ref:`list_software_slidingwindow_1410` - :ref:`list_software_smafa_520` - :ref:`list_software_smallgenomeutilities_2160` - :ref:`list_software_SMARTdenovo_1042` - :ref:`list_software_Smoldyn_742` - :ref:`list_software_SMRT-Link_769` - :ref:`list_software_snakemake_944` - :ref:`list_software_SNAP_306` - :ref:`list_software_SNAPE-pooled_1063` - :ref:`list_software_snaphu_655` - :ref:`list_software_snappy_667` - :ref:`list_software_snippy_675` - :ref:`list_software_snpEff_610` - :ref:`list_software_SNPhylo_685` - :ref:`list_software_SOAPaligner_1045` - :ref:`list_software_SOAPdenovo-Trans_1523` - :ref:`list_software_SOAPdenovo2_1008` - :ref:`list_software_SOAPfuse_742` - :ref:`list_software_socat_538` - :ref:`list_software_SolexaQA++_852` - :ref:`list_software_SortMeRNA_827` - :ref:`list_software_Spack_498` - :ref:`list_software_SPAdes_544` - :ref:`list_software_spaln_542` - :ref:`list_software_Spark_513` - :ref:`list_software_sparsehash_1074` - :ref:`list_software_spectral.methods_1664` - :ref:`list_software_spglib_641` - :ref:`list_software_spglib-python_1360` - :ref:`list_software_Sphinx_634` - :ref:`list_software_SpiceyPy_822` - :ref:`list_software_SpiecEasi_886` - :ref:`list_software_SPLASH_459` - :ref:`list_software_SpliceMap_894` - :ref:`list_software_splitRef_841` - :ref:`list_software_SPRNG_394` - :ref:`list_software_Spyder_631` - :ref:`list_software_SQLite_562` - :ref:`list_software_SqueezeMeta_1129` - :ref:`list_software_SRA-Toolkit_1017` - :ref:`list_software_SRPRISM_560` - :ref:`list_software_SSAHA2_418` - :ref:`list_software_SSPACE_Basic_1024` - :ref:`list_software_Stacks_617` - :ref:`list_software_STAMP_389` - :ref:`list_software_StaMPS_536` - :ref:`list_software_Stampy_638` - :ref:`list_software_STAR_314` - :ref:`list_software_STAR-Fusion_987` - :ref:`list_software_Stata_509` - :ref:`list_software_statsmodels_1203` - :ref:`list_software_STIR_322` - :ref:`list_software_STREAM_460` - :ref:`list_software_strelka_758` - :ref:`list_software_StringTie_921` - :ref:`list_software_Structure_977` - :ref:`list_software_Subread_710` - :ref:`list_software_Subversion_1072` - :ref:`list_software_suds_447` - :ref:`list_software_SuiteSparse_1144` - :ref:`list_software_SUMACLUST_705` - :ref:`list_software_SUMATRA_541` - :ref:`list_software_SUNDIALS_611` - :ref:`list_software_SuperLU_688` - :ref:`list_software_supermagic_1072` - :ref:`list_software_supernova_995` - :ref:`list_software_SVDetect_770` - :ref:`list_software_SVDquest_799` - :ref:`list_software_swarm_554` - :ref:`list_software_SWASH_390` - :ref:`list_software_SWIG_314` - :ref:`list_software_SymEngine_911` - :ref:`list_software_sympy_578` - :ref:`list_software_Szip_422` +:ref:`list_software_S-Lang_514` - :ref:`list_software_S4_135` - :ref:`list_software_SAGE_288` - :ref:`list_software_Sailfish_819` - :ref:`list_software_SALib_427` - :ref:`list_software_Salmon_618` - :ref:`list_software_SALMON-TDDFT_877` - :ref:`list_software_Sambamba_788` - :ref:`list_software_Samcef_591` - :ref:`list_software_samclip_745` - :ref:`list_software_SAMtools_786` - :ref:`list_software_SAS_231` - :ref:`list_software_savvy_569` - :ref:`list_software_Saxon-HE_707` - :ref:`list_software_sbt_329` - :ref:`list_software_ScaLAPACK_707` - :ref:`list_software_Scalasca_795` - :ref:`list_software_SCALCE_427` - :ref:`list_software_sciClone_816` - :ref:`list_software_ScientificPython_1667` - :ref:`list_software_scikit-allel_1214` - :ref:`list_software_scikit-build_1220` - :ref:`list_software_scikit-image_1207` - :ref:`list_software_scikit-learn_1222` - :ref:`list_software_scikit-multilearn_1777` - :ref:`list_software_scikit-optimize_1573` - :ref:`list_software_SCIPhI_480` - :ref:`list_software_scipy_552` - :ref:`list_software_SciPy-bundle_1167` - :ref:`list_software_SCnorm_594` - :ref:`list_software_Scoary_625` - :ref:`list_software_SCons_486` - :ref:`list_software_SCOOP_388` - :ref:`list_software_Score-P_633` - :ref:`list_software_SCOTCH_452` - :ref:`list_software_scp_326` - :ref:`list_software_Scrappie_823` - :ref:`list_software_scVelo_620` - :ref:`list_software_SDCC_285` - :ref:`list_software_SDL2_277` - :ref:`list_software_Seaborn_714` - :ref:`list_software_SearchGUI_827` - :ref:`list_software_SECAPR_446` - :ref:`list_software_segemehl_842` - :ref:`list_software_segmentation-models_1983` - :ref:`list_software_SelEstim_806` - :ref:`list_software_SentencePiece_1307` - :ref:`list_software_sep_328` - :ref:`list_software_SEPP_312` - :ref:`list_software_Seq-Gen_624` - :ref:`list_software_seq2HLA_592` - :ref:`list_software_SeqAn_472` - :ref:`list_software_SeqAn3_523` - :ref:`list_software_Seqmagick_917` - :ref:`list_software_SeqPrep_704` - :ref:`list_software_seqtk_552` - :ref:`list_software_Serf_400` - :ref:`list_software_setuptools_1122` - :ref:`list_software_Seurat_628` - :ref:`list_software_Shannon_725` - :ref:`list_software_shapAAR_640` - :ref:`list_software_SHAPEIT_526` - :ref:`list_software_Shapely_726` - :ref:`list_software_sharutils_991` - :ref:`list_software_shift_542` - :ref:`list_software_SHORE_385` - :ref:`list_software_Short-Pair_969` - :ref:`list_software_shovill_769` - :ref:`list_software_shrinkwrap_1097` - :ref:`list_software_Sibelia_697` - :ref:`list_software_sickle_635` - :ref:`list_software_Siesta_617` - :ref:`list_software_SimPEG_517` - :ref:`list_software_SIMPLE_458` - :ref:`list_software_SimpleElastix_1348` - :ref:`list_software_SimpleITK_850` - :ref:`list_software_simpy_562` - :ref:`list_software_SimVascular_1130` - :ref:`list_software_SingleM_687` - :ref:`list_software_Singular_837` - :ref:`list_software_Singularity_1179` - :ref:`list_software_SIONlib_624` - :ref:`list_software_SIP_236` - :ref:`list_software_SKESA_375` - :ref:`list_software_sketchmap_960` - :ref:`list_software_skewer_657` - :ref:`list_software_SLATEC_444` - :ref:`list_software_SLEPc_407` - :ref:`list_software_slepc4py_820` - :ref:`list_software_sleuth_661` - :ref:`list_software_slidingwindow_1410` - :ref:`list_software_smafa_520` - :ref:`list_software_smallgenomeutilities_2160` - :ref:`list_software_SMARTdenovo_1042` - :ref:`list_software_Smoldyn_742` - :ref:`list_software_SMRT-Link_769` - :ref:`list_software_snakemake_944` - :ref:`list_software_SNAP_306` - :ref:`list_software_SNAPE-pooled_1063` - :ref:`list_software_snaphu_655` - :ref:`list_software_snappy_667` - :ref:`list_software_snippy_675` - :ref:`list_software_snpEff_610` - :ref:`list_software_SNPhylo_685` - :ref:`list_software_SOAPaligner_1045` - :ref:`list_software_SOAPdenovo-Trans_1523` - :ref:`list_software_SOAPdenovo2_1008` - :ref:`list_software_SOAPfuse_742` - :ref:`list_software_socat_538` - :ref:`list_software_SolexaQA++_852` - :ref:`list_software_SortMeRNA_827` - :ref:`list_software_Spack_498` - :ref:`list_software_SPAdes_544` - :ref:`list_software_spaln_542` - :ref:`list_software_Spark_513` - :ref:`list_software_sparsehash_1074` - :ref:`list_software_spatialreg_1068` - :ref:`list_software_spectral.methods_1664` - :ref:`list_software_spglib_641` - :ref:`list_software_spglib-python_1360` - :ref:`list_software_Sphinx_634` - :ref:`list_software_SpiceyPy_822` - :ref:`list_software_SpiecEasi_886` - :ref:`list_software_SPLASH_459` - :ref:`list_software_SpliceMap_894` - :ref:`list_software_split-seq_930` - :ref:`list_software_splitRef_841` - :ref:`list_software_spoa_435` - :ref:`list_software_SPRNG_394` - :ref:`list_software_Spyder_631` - :ref:`list_software_SQLite_562` - :ref:`list_software_SqueezeMeta_1129` - :ref:`list_software_SRA-Toolkit_1017` - :ref:`list_software_SRPRISM_560` - :ref:`list_software_SSAHA2_418` - :ref:`list_software_SSN_244` - :ref:`list_software_SSPACE_Basic_1024` - :ref:`list_software_Stacks_617` - :ref:`list_software_STAMP_389` - :ref:`list_software_StaMPS_536` - :ref:`list_software_Stampy_638` - :ref:`list_software_STAR_314` - :ref:`list_software_STAR-Fusion_987` - :ref:`list_software_Stata_509` - :ref:`list_software_statsmodels_1203` - :ref:`list_software_STEAK_376` - :ref:`list_software_STIR_322` - :ref:`list_software_stpipeline_1085` - :ref:`list_software_STREAM_460` - :ref:`list_software_strelka_758` - :ref:`list_software_StringTie_921` - :ref:`list_software_Structure_977` - :ref:`list_software_Subread_710` - :ref:`list_software_Subversion_1072` - :ref:`list_software_suds_447` - :ref:`list_software_SuiteSparse_1144` - :ref:`list_software_SUMACLUST_705` - :ref:`list_software_SUMATRA_541` - :ref:`list_software_SUNDIALS_611` - :ref:`list_software_SuperLU_688` - :ref:`list_software_supermagic_1072` - :ref:`list_software_supernova_995` - :ref:`list_software_SVDetect_770` - :ref:`list_software_SVDquest_799` - :ref:`list_software_SVG_240` - :ref:`list_software_swarm_554` - :ref:`list_software_SWASH_390` - :ref:`list_software_SWIG_314` - :ref:`list_software_SymEngine_911` - :ref:`list_software_sympy_578` - :ref:`list_software_Szip_422` .. _list_software_S-Lang_514: @@ -26798,11 +28412,12 @@ Sailfish is a software tool that implements a novel, alignment-free algorithm fo *homepage*: http://www.cs.cmu.edu/~ckingsf/software/sailfish/ -========== ================== ============== -version versionsuffix toolchain -========== ================== ============== -``0.10.1`` ``-Python-2.7.12`` ``foss/2016b`` -========== ================== ============== +========== ================== =============== +version versionsuffix toolchain +========== ================== =============== +``0.10.1`` ``gompi/2019b`` +``0.10.1`` ``-Python-2.7.12`` ``foss/2016b`` +========== ================== =============== .. _list_software_SALib_427: @@ -26830,17 +28445,18 @@ Salmon is a wicked-fast program to produce a highly-accurate, transcript-level *homepage*: https://github.com/COMBINE-lab/salmon -========== ================== =============== -version versionsuffix toolchain -========== ================== =============== -``0.8.2`` ``system`` -``0.8.2`` ``-Python-2.7.12`` ``foss/2016b`` -``0.11.2`` ``intel/2018a`` -``0.12.0`` ``foss/2018b`` -``0.14.1`` ``foss/2018b`` -``0.14.2`` ``gompi/2019a`` -``1.0.0`` ``gompi/2019a`` -========== ================== =============== +========== ================== ================================ +version versionsuffix toolchain +========== ================== ================================ +``0.8.2`` ``system`` +``0.8.2`` ``-Python-2.7.12`` ``foss/2016b`` +``0.11.2`` ``intel/2018a`` +``0.12.0`` ``foss/2018b`` +``0.14.1`` ``foss/2018b`` +``0.14.2`` ``gompi/2019a`` +``1.0.0`` ``gompi/2019a``, ``gompi/2019b`` +``1.1.0`` ``gompi/2019b`` +========== ================== ================================ .. _list_software_SALMON-TDDFT_877: @@ -26922,7 +28538,7 @@ version versionsuffix toolchain ========== ================= ======================================================================================================================================= ``0.1.17`` ``intel/2017a`` ``0.1.19`` ``foss/2016a``, ``foss/2016b`` -``0.1.20`` ``foss/2018b``, ``intel/2017a``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b`` +``0.1.20`` ``GCC/8.3.0``, ``foss/2018b``, ``intel/2017a``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b``, ``intel/2019b`` ``1.2`` ``foss/2016b`` ``1.3`` ``foss/2016a``, ``intel/2016a`` ``1.3.1`` ``foss/2016a``, ``foss/2016b``, ``intel/2016a``, ``intel/2016b`` @@ -26934,7 +28550,7 @@ version versionsuffix toolchain ``1.7`` ``foss/2018a``, ``intel/2018a`` ``1.8`` ``intel/2018a`` ``1.9`` ``GCC/6.4.0-2.28``, ``GCC/7.3.0-2.30``, ``GCC/8.2.0-2.31.1``, ``foss/2018b``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``intel/2018b`` -``1.10`` ``GCC/8.2.0-2.31.1`` +``1.10`` ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0``, ``iccifort/2019.5.281`` ========== ================= ======================================================================================================================================= @@ -27110,6 +28726,22 @@ version versionsuffix toolchain ========= ================== ============== +.. _list_software_scikit-build_1220: + +*scikit-build* +++++++++++++++ + +Scikit-Build, or skbuild, is an improved build system generator for CPython C/C++/Fortran/Cython extensions. + +*homepage*: https://scikit-build.github.io + +========== ================= =============================== +version versionsuffix toolchain +========== ================= =============================== +``0.10.0`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` +========== ================= =============================== + + .. _list_software_scikit-image_1207: *scikit-image* @@ -27134,7 +28766,7 @@ version versionsuffix toolchain ``0.14.0`` ``-Python-3.6.4`` ``intel/2018a`` ``0.14.1`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b`` ``0.15.0`` ``-Python-3.7.2`` ``foss/2019a`` -``0.16.2`` ``-Python-3.7.4`` ``foss/2019b`` +``0.16.2`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` ========== ================== =================================================== @@ -27172,7 +28804,8 @@ version versionsuffix toolchain ``0.20.2`` ``-Python-2.7.15`` ``foss/2018b`` ``0.20.2`` ``-Python-3.6.6`` ``foss/2018b`` ``0.20.3`` ``foss/2019a``, ``fosscuda/2019a``, ``intel/2019a`` -``0.21.3`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` +``0.20.4`` ``-Python-2.7.16`` ``intel/2019b`` +``0.21.3`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b`` ========== ================================= ======================================================================== @@ -27205,6 +28838,7 @@ Scikit-Optimize, or skopt, is a simple and efficient library to minimize (very) version versionsuffix toolchain ========= ================= =============== ``0.5.2`` ``-Python-3.6.6`` ``intel/2018b`` +``0.7.4`` ``-Python-3.7.4`` ``foss/2019b`` ========= ================= =============== @@ -27255,7 +28889,7 @@ Bundle of Python packages for scientific software version versionsuffix toolchain =========== ================== ======================================================================== ``2019.03`` ``foss/2019a``, ``fosscuda/2019a``, ``intel/2019a``, ``intelcuda/2019a`` -``2019.10`` ``-Python-2.7.16`` ``foss/2019b`` +``2019.10`` ``-Python-2.7.16`` ``foss/2019b``, ``intel/2019b`` ``2019.10`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b`` =========== ================== ======================================================================== @@ -27413,6 +29047,22 @@ version toolchain ========= =============== +.. _list_software_scVelo_620: + +*scVelo* +++++++++ + +scVelo is a scalable toolkit for estimating and analyzing RNA velocities in single cells using dynamical modeling. + +*homepage*: https://scvelo.org + +========== ================= ============== +version versionsuffix toolchain +========== ================= ============== +``0.1.24`` ``-Python-3.7.4`` ``foss/2019b`` +========== ================= ============== + + .. _list_software_SDCC_285: *SDCC* @@ -27456,19 +29106,20 @@ Seaborn is a Python visualization library based on matplotlib. It provides a h *homepage*: http://stanford.edu/~mwaskom/software/seaborn/ -========= ================== ========================================================================================= -version versionsuffix toolchain -========= ================== ========================================================================================= -``0.7.1`` ``-Python-2.7.12`` ``intel/2016b`` -``0.8.1`` ``-Python-2.7.13`` ``foss/2017a`` -``0.8.1`` ``-Python-2.7.14`` ``intel/2018a`` -``0.9.0`` ``-Python-2.7.14`` ``foss/2017b``, ``fosscuda/2017b``, ``intel/2017b``, ``intel/2018a``, ``intelcuda/2017b`` -``0.9.0`` ``-Python-2.7.15`` ``foss/2018b``, ``foss/2019a``, ``intel/2018b``, ``intel/2019a`` -``0.9.0`` ``-Python-3.6.3`` ``foss/2017b``, ``fosscuda/2017b``, ``intel/2017b``, ``intelcuda/2017b`` -``0.9.0`` ``-Python-3.6.4`` ``intel/2018a`` -``0.9.0`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` -``0.9.0`` ``-Python-3.7.2`` ``foss/2019a``, ``intel/2019a`` -========= ================== ========================================================================================= +========== ================== ========================================================================================= +version versionsuffix toolchain +========== ================== ========================================================================================= +``0.7.1`` ``-Python-2.7.12`` ``intel/2016b`` +``0.8.1`` ``-Python-2.7.13`` ``foss/2017a`` +``0.8.1`` ``-Python-2.7.14`` ``intel/2018a`` +``0.9.0`` ``-Python-2.7.14`` ``foss/2017b``, ``fosscuda/2017b``, ``intel/2017b``, ``intel/2018a``, ``intelcuda/2017b`` +``0.9.0`` ``-Python-2.7.15`` ``foss/2018b``, ``foss/2019a``, ``intel/2018b``, ``intel/2019a`` +``0.9.0`` ``-Python-3.6.3`` ``foss/2017b``, ``fosscuda/2017b``, ``intel/2017b``, ``intelcuda/2017b`` +``0.9.0`` ``-Python-3.6.4`` ``intel/2018a`` +``0.9.0`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` +``0.9.0`` ``-Python-3.7.2`` ``foss/2019a``, ``intel/2019a`` +``0.10.0`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` +========== ================== ========================================================================================= .. _list_software_SearchGUI_827: @@ -27487,6 +29138,22 @@ version versionsuffix toolchain ========= =================== ========== +.. _list_software_SECAPR_446: + +*SECAPR* +++++++++ + +SECAPR is a bioinformatics pipeline for the rapid and user-friendly processing of targeted enriched Illumina sequences, from raw reads to alignments + +*homepage*: https://github.com/AntonelliLab/seqcap_processor + +========== ================== ============== +version versionsuffix toolchain +========== ================== ============== +``1.1.15`` ``-Python-2.7.16`` ``foss/2019b`` +========== ================== ============== + + .. _list_software_segemehl_842: *segemehl* @@ -27504,6 +29171,22 @@ version toolchain ========= ================================================ +.. _list_software_segmentation-models_1983: + +*segmentation-models* ++++++++++++++++++++++ + +Python library with Neural Networks for Image Segmentation based on Keras and TensorFlow. + +*homepage*: https://github.com/qubvel/segmentation_models + +========= ================= ================================== +version versionsuffix toolchain +========= ================= ================================== +``1.0.1`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` +========= ================= ================================== + + .. _list_software_SelEstim_806: *SelEstim* @@ -27520,6 +29203,22 @@ version versionsuffix toolchain ========= ================= ========== +.. _list_software_SentencePiece_1307: + +*SentencePiece* ++++++++++++++++ + +Unsupervised text tokenizer for Neural Network-based text generation. + +*homepage*: https://github.com/google/sentencepiece + +========== ================= ============= +version versionsuffix toolchain +========== ================= ============= +``0.1.85`` ``-Python-3.7.4`` ``GCC/8.3.0`` +========== ================= ============= + + .. _list_software_sep_328: *sep* @@ -27536,6 +29235,22 @@ version versionsuffix toolchain ========= ================== =============================== +.. _list_software_SEPP_312: + +*SEPP* +++++++ + +SATe-enabled Phylogenetic Placement - addresses the problem of phylogenetic placement of short reads into reference alignments and trees. + +*homepage*: https://github.com/smirarab/sepp + +========== ================= ============== +version versionsuffix toolchain +========== ================= ============== +``4.3.10`` ``-Python-3.7.4`` ``foss/2019b`` +========== ================= ============== + + .. _list_software_Seq-Gen_624: *Seq-Gen* @@ -27578,12 +29293,13 @@ SeqAn is an open source C++ library of efficient algorithms and data structures *homepage*: https://www.seqan.de/ -========= ===================================================== -version toolchain -========= ===================================================== -``2.3.2`` ``foss/2016b`` -``2.4.0`` ``GCC/8.2.0-2.31.1``, ``foss/2018b``, ``intel/2018b`` -========= ===================================================== +========= ============= ===================================================== +version versionsuffix toolchain +========= ============= ===================================================== +``1.4.2`` ``-library`` ``system`` +``2.3.2`` ``foss/2016b`` +``2.4.0`` ``GCC/8.2.0-2.31.1``, ``foss/2018b``, ``intel/2018b`` +========= ============= ===================================================== .. _list_software_SeqAn3_523: @@ -27644,12 +29360,12 @@ Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FA *homepage*: https://github.com/lh3/seqtk/ -======= ==================================================== -version toolchain -======= ==================================================== -``1.2`` ``foss/2016b``, ``intel/2017a`` -``1.3`` ``GCC/8.2.0-2.31.1``, ``foss/2018a``, ``foss/2018b`` -======= ==================================================== +======= =================================================================== +version toolchain +======= =================================================================== +``1.2`` ``foss/2016b``, ``intel/2017a`` +``1.3`` ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0``, ``foss/2018a``, ``foss/2018b`` +======= =================================================================== .. _list_software_Serf_400: @@ -27692,7 +29408,7 @@ version versionsuffix toolchain Seurat is an R package designed for QC, analysis, and exploration of single cell RNA-seq data. -*homepage*: http://satijalab.org/seurat +*homepage*: https://satijalab.org/seurat ============ ============= =============== version versionsuffix toolchain @@ -27700,6 +29416,7 @@ version versionsuffix toolchain ``1.4.0.16`` ``-R-3.4.0`` ``intel/2017a`` ``2.3.4`` ``-R-3.4.4`` ``intel/2018a`` ``2.3.4`` ``-R-3.5.1`` ``foss/2018b`` +``3.1.2`` ``-R-3.6.0`` ``foss/2019a`` ============ ============= =============== @@ -27752,6 +29469,22 @@ version versionsuffix toolchain ========== =============== ========== +.. _list_software_Shapely_726: + +*Shapely* ++++++++++ + +Shapely is a BSD-licensed Python package for manipulation and analysis of planar geometric objects. It is based on the widely deployed GEOS (the engine of PostGIS) and JTS (from which GEOS is ported) libraries. + +*homepage*: https://github.com/Toblerity/Shapely + +========= ================= ====================================== +version versionsuffix toolchain +========= ================= ====================================== +``1.7.0`` ``-Python-3.7.4`` ``GCC/8.3.0``, ``iccifort/2019.5.281`` +========= ================= ====================================== + + .. _list_software_sharutils_991: *sharutils* @@ -27891,15 +29624,17 @@ SIESTA is both a method and its computer program implementation, to perform effi *homepage*: http://departments.icmab.es/leem/siesta -========== =============================== -version toolchain -========== =============================== -``4.0`` ``intel/2017a`` -``4.0.1`` ``intel/2017a`` -``4.1-b2`` ``intel/2017a`` -``4.1-b3`` ``intel/2017a`` -``4.1-b4`` ``foss/2018b``, ``intel/2018b`` -========== =============================== +=============== ============= =============================== +version versionsuffix toolchain +=============== ============= =============================== +``4.0`` ``intel/2017a`` +``4.0.1`` ``intel/2017a`` +``4.1-b2`` ``intel/2017a`` +``4.1-b3`` ``intel/2017a`` +``4.1-b4`` ``foss/2018b``, ``intel/2018b`` +``4.1-MaX-1.0`` ``intel/2019b`` +``4.1-MaX-1.0`` ``-PEXSI`` ``intel/2019b`` +=============== ============= =============================== .. _list_software_SimPEG_517: @@ -27939,15 +29674,16 @@ version toolchain *SimpleElastix* +++++++++++++++ -Multi-lingual medical image registration library. +Multi-lingual medical image registration library. -*homepage*: http://simpleelastix.github.io/ +*homepage*: https://simpleelastix.github.io ========== ================= ============== version versionsuffix toolchain ========== ================= ============== ``0.10.0`` ``-Python-3.6.3`` ``foss/2017b`` ``0.10.0`` ``-Python-3.6.4`` ``foss/2018a`` +``1.1.0`` ``-Python-3.7.4`` ``foss/2019b`` ========== ================= ============== @@ -27966,6 +29702,7 @@ version versionsuffix toolchain ``1.1.0`` ``-Python-2.7.15`` ``foss/2018b`` ``1.1.0`` ``-Python-3.6.4`` ``foss/2018a`` ``1.1.0`` ``-Python-3.6.6`` ``foss/2018b`` +``1.2.4`` ``-Python-3.7.4`` ``foss/2019b`` ========= ================== ============== @@ -28018,6 +29755,22 @@ version versionsuffix toolchain ========== ================== =============== +.. _list_software_Singular_837: + +*Singular* +++++++++++ + +Singular is a computer algebra system for polynomial computations, with special emphasis on commutative and non-commutative algebra, algebraic geometry, and singularity theory. + +*homepage*: https://www.singular.uni-kl.de/ + +========= ========== +version toolchain +========= ========== +``4.1.2`` ``system`` +========= ========== + + .. _list_software_Singularity_1179: *Singularity* @@ -28129,6 +29882,22 @@ version toolchain ========= =============== +.. _list_software_SLATEC_444: + +*SLATEC* +++++++++ + +SLATEC Common Mathematical Library, a comprehensive software library containing over 1400 general purpose mathematical and statistical routines written in Fortran 77. + +*homepage*: https://www.netlib.org/slatec/ + +======= ========================================================== +version toolchain +======= ========================================================== +``4.1`` ``GCC/6.4.0-2.28``, ``iccifort/2018.1.163-GCC-6.4.0-2.28`` +======= ========================================================== + + .. _list_software_SLEPc_407: *SLEPc* @@ -28136,15 +29905,16 @@ version toolchain SLEPc (Scalable Library for Eigenvalue Problem Computations) is a software library for the solution of large scale sparse eigenvalue problems on parallel computers. It is an extension of PETSc and can be used for either standard or generalized eigenproblems, with real or complex arithmetic. It can also be used for computing a partial SVD of a large, sparse, rectangular matrix, and to solve quadratic eigenvalue problems. -*homepage*: http://www.grycap.upv.es/slepc/ +*homepage*: https://www.grycap.upv.es/slepc/ -========== ============== -version toolchain -========== ============== -``3.8.3`` ``foss/2017b`` -``3.9.2`` ``foss/2018a`` -``3.11.0`` ``foss/2018b`` -========== ============== +========== =============================== +version toolchain +========== =============================== +``3.8.3`` ``foss/2017b`` +``3.9.2`` ``foss/2018a`` +``3.11.0`` ``foss/2018b`` +``3.12.2`` ``foss/2019b``, ``intel/2019b`` +========== =============================== .. _list_software_slepc4py_820: @@ -28555,16 +30325,18 @@ Genome assembler for single-cell and isolates data sets *homepage*: http://bioinf.spbau.ru/en/spades -========== ============================================== -version toolchain -========== ============================================== -``3.9.0`` ``foss/2016a``, ``foss/2016b`` -``3.10.1`` ``foss/2016b``, ``foss/2017a`` -``3.11.1`` ``foss/2017b``, ``foss/2018a`` -``3.12.0`` ``foss/2016b``, ``foss/2018a``, ``foss/2018b`` -``3.13.0`` ``foss/2018b`` -``3.13.1`` ``GCC/8.2.0-2.31.1`` -========== ============================================== +========== ================= ============================================== +version versionsuffix toolchain +========== ================= ============================================== +``3.9.0`` ``foss/2016a``, ``foss/2016b`` +``3.10.1`` ``foss/2016b``, ``foss/2017a`` +``3.11.1`` ``foss/2017b``, ``foss/2018a`` +``3.12.0`` ``foss/2016b``, ``foss/2018a``, ``foss/2018b`` +``3.13.0`` ``foss/2018b`` +``3.13.1`` ``GCC/8.2.0-2.31.1`` +``3.14.0`` ``-Python-3.7.2`` ``GCC/8.2.0-2.31.1`` +``3.14.0`` ``-Python-3.7.4`` ``GCC/8.3.0`` +========== ================= ============================================== .. _list_software_spaln_542: @@ -28622,12 +30394,28 @@ An extremely memory-efficient hash_map implementation. 2 bits/entry overhead! T *homepage*: https://github.com/sparsehash/sparsehash -========= =========================================================================================================== -version toolchain -========= =========================================================================================================== -``2.0.2`` ``foss/2016a`` -``2.0.3`` ``GCCcore/5.4.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``foss/2016b``, ``intel/2017a`` -========= =========================================================================================================== +========= ============================================================================================================================== +version toolchain +========= ============================================================================================================================== +``2.0.2`` ``foss/2016a`` +``2.0.3`` ``GCCcore/5.4.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``foss/2016b``, ``intel/2017a`` +========= ============================================================================================================================== + + +.. _list_software_spatialreg_1068: + +*spatialreg* +++++++++++++ + +A collection of all the estimation functions for spatial cross-sectional models (on lattice/areal data using spatial weights matrices) contained up to now in 'spdep', 'sphet' and 'spse'. + +*homepage*: https://cran.r-project.org/package=spatialreg + +========= ============= ============== +version versionsuffix toolchain +========= ============= ============== +``1.1-5`` ``-R-3.6.2`` ``foss/2019b`` +========= ============= ============== .. _list_software_spectral.methods_1664: @@ -28776,6 +30564,22 @@ version toolchain =========== ================== +.. _list_software_split-seq_930: + +*split-seq* ++++++++++++ + +Analysis tools for split-seq. + +*homepage*: https://github.com/yjzhang/split-seq-pipeline + +============ ================= ============== +version versionsuffix toolchain +============ ================= ============== +``20190717`` ``-Python-3.6.6`` ``foss/2018b`` +============ ================= ============== + + .. _list_software_splitRef_841: *splitRef* @@ -28792,6 +30596,22 @@ version toolchain ========= ========== +.. _list_software_spoa_435: + +*spoa* +++++++ + +Spoa (SIMD POA) is a c++ implementation of the partial order alignment (POA) algorithm which is used to generate consensus sequences + +*homepage*: https://github.com/rvaser/spoa + +========= ================== +version toolchain +========= ================== +``3.0.1`` ``GCC/7.3.0-2.30`` +========= ================== + + .. _list_software_SPRNG_394: *SPRNG* @@ -28927,6 +30747,22 @@ version versionsuffix toolchain ========= ============= ========== +.. _list_software_SSN_244: + +*SSN* ++++++ + +Spatial statistical modeling and prediction for data on stream networks, including models based on in-stream distance. Models are created using moving average constructions. Spatial linear models, including explanatory variables, can be fit with (restricted) maximum likelihood. Mapping and other graphical functions are included. + +*homepage*: https://cran.r-project.org/web/packages/SSN + +========== ============= ============== +version versionsuffix toolchain +========== ============= ============== +``1.1.14`` ``-R-3.6.0`` ``foss/2019a`` +========== ============= ============== + + .. _list_software_SSPACE_Basic_1024: *SSPACE_Basic* @@ -28971,6 +30807,7 @@ version toolchain ``2.2`` ``foss/2018a`` ``2.3b`` ``foss/2018a`` ``2.3e`` ``foss/2018b`` +``2.5`` ``iccifort/2019.5.281`` ``2.41`` ``GCC/8.2.0-2.31.1``, ``foss/2018b``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1`` ============== ============================================================================== @@ -29048,6 +30885,8 @@ version toolchain ``2.7.0d`` ``foss/2018b`` ``2.7.0f`` ``GCC/8.2.0-2.31.1``, ``foss/2018b`` ``2.7.1a`` ``GCC/8.2.0-2.31.1``, ``foss/2018b`` +``2.7.2b`` ``GCC/8.3.0`` +``2.7.3a`` ``GCC/8.3.0`` ========== =============================================== @@ -29056,7 +30895,7 @@ version toolchain *STAR-Fusion* +++++++++++++ -STAR-Fusion uses the STAR aligner to identify candidate fusion transcripts supported by Illumina reads. STAR-Fusion further processes the output generated by the STAR aligner to map junction reads and spanning reads to a reference annotation set. +STAR-Fusion uses the STAR aligner to identify candidate fusion transcripts supported by Illumina reads. STAR-Fusion further processes the output generated by the STAR aligner to map junction reads and spanning reads to a reference annotation set. *homepage*: https://github.com/STAR-Fusion/STAR-Fusion @@ -29065,6 +30904,7 @@ version versionsuffix toolchain ========= ============================= ==================== ``1.5.0`` ``-Perl-5.28.0`` ``foss/2018b`` ``1.6.0`` ``-Perl-5.28.1-Python-3.7.2`` ``GCC/8.2.0-2.31.1`` +``1.8.1`` ``-Python-3.7.4`` ``foss/2019b`` ========= ============================= ==================== @@ -29077,11 +30917,12 @@ Stata is a complete, integrated statistical software package that provides every *homepage*: https://www.stata.com/ -======= ========== -version toolchain -======= ========== -``15`` ``system`` -======= ========== +======= ============= ========== +version versionsuffix toolchain +======= ============= ========== +``15`` ``system`` +``16`` ``-legacy`` ``system`` +======= ============= ========== .. _list_software_statsmodels_1203: @@ -29101,10 +30942,28 @@ version versionsuffix toolchain ``0.6.1`` ``-Python-3.5.2`` ``intel/2016b`` ``0.8.0`` ``-Python-2.7.13`` ``intel/2017a`` ``0.9.0`` ``-Python-2.7.15`` ``foss/2018b``, ``intel/2018b`` +``0.9.0`` ``-Python-3.6.6`` ``intel/2018b`` ``0.10.1`` ``foss/2019a`` +``0.11.0`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` ========== ================== =============================== +.. _list_software_STEAK_376: + +*STEAK* ++++++++ + +Detects integrations of any sort in high-throughput sequencing (HTS) data. STEAK was built for validating and discovering transposable element (TE) and retroviral integrations in a variety of HTS data. The software performs on both single-end (SE) and paired-end ( PE) libraries and on a variety of HTS sequencing strategies. It can be applied to a broad range of research interests and clinical uses such as population genetic studies and detecting polymorphic integrations. + +*homepage*: https://omictools.com/steak-tool + +============== ================== ============== +version versionsuffix toolchain +============== ================== ============== +``2019.09.12`` ``-Python-2.7.16`` ``foss/2019b`` +============== ================== ============== + + .. _list_software_STIR_322: *STIR* @@ -29121,6 +30980,23 @@ version toolchain ======= =============== +.. _list_software_stpipeline_1085: + +*stpipeline* +++++++++++++ + +The ST Pipeline contains the tools and scripts needed to process and analyze the raw files generated with the Spatial Transcriptomics method in FASTQ format to generated datasets for down-stream analysis. The ST pipeline can also be used to process single cell data as long as a file with barcodes identifying each cell is provided. The ST Pipeline can also process RNA-Seq datasets generated with or without UMIs. + +*homepage*: https://github.com/SpatialTranscriptomicsResearch/st_pipeline + +========= ================== ============== +version versionsuffix toolchain +========= ================== ============== +``1.7.3`` ``-Python-2.7.15`` ``foss/2018b`` +``1.7.6`` ``-Python-3.7.2`` ``foss/2019a`` +========= ================== ============== + + .. _list_software_STREAM_460: *STREAM* @@ -29160,9 +31036,9 @@ version versionsuffix toolchain *StringTie* +++++++++++ -StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. +StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts -*homepage*: http://ccb.jhu.edu/software/%(namelower)/ +*homepage*: https://ccb.jhu.edu/software/stringtie/ ========== ================================== version toolchain @@ -29172,6 +31048,7 @@ version toolchain ``1.3.3b`` ``foss/2016b`` ``1.3.5`` ``GCCcore/8.2.0``, ``foss/2018b`` ``2.0.3`` ``GCCcore/7.3.0`` +``2.1.0`` ``foss/2018b`` ========== ================================== @@ -29184,11 +31061,11 @@ The program structure is a free software package for using multi-locus genotype *homepage*: https://web.stanford.edu/group/pritchardlab/structure.html -========= ====================================== -version toolchain -========= ====================================== -``2.3.4`` ``iccifort/2019.3.199-GCC-8.3.0-2.32`` -========= ====================================== +========= ============================================================ +version toolchain +========= ============================================================ +``2.3.4`` ``GCC/8.2.0-2.31.1``, ``iccifort/2019.3.199-GCC-8.3.0-2.32`` +========= ============================================================ .. _list_software_Subread_710: @@ -29200,14 +31077,14 @@ High performance read alignment, quantification and mutation discovery *homepage*: http://subread.sourceforge.net/ -============ ============================== -version toolchain -============ ============================== -``1.5.0-p1`` ``foss/2016a``, ``foss/2016b`` -``1.6.3`` ``foss/2018b`` -``1.6.4`` ``foss/2018b`` -``2.0.0`` ``GCC/7.3.0-2.30`` -============ ============================== +============ ================================= +version toolchain +============ ================================= +``1.5.0-p1`` ``foss/2016a``, ``foss/2016b`` +``1.6.3`` ``foss/2018b`` +``1.6.4`` ``foss/2018b`` +``2.0.0`` ``GCC/7.3.0-2.30``, ``GCC/8.3.0`` +============ ================================= .. _list_software_Subversion_1072: @@ -29267,7 +31144,7 @@ version versionsuffix toolchain ``5.1.2`` ``-METIS-5.1.0`` ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b`` ``5.1.2`` ``-ParMETIS-4.0.3`` ``foss/2017b``, ``intel/2017b`` ``5.4.0`` ``-METIS-5.1.0`` ``foss/2019a``, ``intel/2018b``, ``intel/2019a`` -``5.6.0`` ``-METIS-5.1.0`` ``foss/2019b`` +``5.6.0`` ``-METIS-5.1.0`` ``foss/2019b``, ``intel/2019b`` ========= =================== ================================================================================================= @@ -29347,11 +31224,11 @@ Very simple MPI sanity code. Nothing more, nothing less. *homepage*: https://github.com/hpc/supermagic -============ ============== -version toolchain -============ ============== -``20170824`` ``foss/2017a`` -============ ============== +============ =============================== +version toolchain +============ =============================== +``20170824`` ``foss/2017a``, ``gompi/2019b`` +============ =============================== .. _list_software_supernova_995: @@ -29403,6 +31280,22 @@ version toolchain ============ =============== +.. _list_software_SVG_240: + +*SVG* ++++++ + +Perl binding for SVG + +*homepage*: https://metacpan.org/pod/SVG + +======== ================ ============== +version versionsuffix toolchain +======== ================ ============== +``2.84`` ``-Perl-5.30.0`` ``foss/2019b`` +======== ================ ============== + + .. _list_software_swarm_554: *swarm* @@ -29528,7 +31421,7 @@ version toolchain --- -:ref:`list_software_tabix_536` - :ref:`list_software_taco_423` - :ref:`list_software_TagLib_563` - :ref:`list_software_TAMkin_548` - :ref:`list_software_taxator-tk_1039` - :ref:`list_software_tbb_312` - :ref:`list_software_tbl2asn_694` - :ref:`list_software_TCC_218` - :ref:`list_software_Tcl_291` - :ref:`list_software_tcsh_434` - :ref:`list_software_tecplot360ex_1137` - :ref:`list_software_TensorFlow_1043` - :ref:`list_software_TensorRT_801` - :ref:`list_software_Tesla-Deployment-Kit_1948` - :ref:`list_software_tesseract_974` - :ref:`list_software_testpath_877` - :ref:`list_software_TetGen_583` - :ref:`list_software_TEToolkit_895` - :ref:`list_software_texinfo_765` - :ref:`list_software_Text-CSV_702` - :ref:`list_software_Theano_607` - :ref:`list_software_THetA_438` - :ref:`list_software_thurstonianIRT_1454` - :ref:`list_software_TiCCutils_884` - :ref:`list_software_Tika_393` - :ref:`list_software_TiMBL_408` - :ref:`list_software_time_431` - :ref:`list_software_TINKER_461` - :ref:`list_software_TinyDB_554` - :ref:`list_software_Tk_191` - :ref:`list_software_Tkinter_737` - :ref:`list_software_TM-align_729` - :ref:`list_software_tmux_462` - :ref:`list_software_ToFu_382` - :ref:`list_software_TopHat_592` - :ref:`list_software_torchvision_1208` - :ref:`list_software_TotalView_927` - :ref:`list_software_tqdm_438` - :ref:`list_software_Tracer_609` - :ref:`list_software_TransDecoder_1214` - :ref:`list_software_Transrate_948` - :ref:`list_software_travis_665` - :ref:`list_software_TreeMix_702` - :ref:`list_software_TreeShrink_1023` - :ref:`list_software_TRF_236` - :ref:`list_software_Triangle_822` - :ref:`list_software_Trilinos_852` - :ref:`list_software_Trim_Galore_1109` - :ref:`list_software_trimAl_617` - :ref:`list_software_Trimmomatic_1158` - :ref:`list_software_Trinity_755` - :ref:`list_software_TRIQS_403` - :ref:`list_software_TRIQS-cthyb_986` - :ref:`list_software_TRIQS-dft_tools_1422` - :ref:`list_software_TRIQS-tprf_892` - :ref:`list_software_TRUST_418` - :ref:`list_software_TurboVNC_755` - :ref:`list_software_TVB_236` - :ref:`list_software_tvb-data_787` - :ref:`list_software_TVB-deps_709` - :ref:`list_software_tvb-framework_1351` - :ref:`list_software_tvb-library_1134` +:ref:`list_software_tabix_536` - :ref:`list_software_taco_423` - :ref:`list_software_TagLib_563` - :ref:`list_software_TAMkin_548` - :ref:`list_software_taxator-tk_1039` - :ref:`list_software_tbb_312` - :ref:`list_software_tbl2asn_694` - :ref:`list_software_TCC_218` - :ref:`list_software_Tcl_291` - :ref:`list_software_tcsh_434` - :ref:`list_software_tecplot360ex_1137` - :ref:`list_software_TensorFlow_1043` - :ref:`list_software_TensorRT_801` - :ref:`list_software_Tesla-Deployment-Kit_1948` - :ref:`list_software_tesseract_974` - :ref:`list_software_testpath_877` - :ref:`list_software_TetGen_583` - :ref:`list_software_TEToolkit_895` - :ref:`list_software_texinfo_765` - :ref:`list_software_Text-CSV_702` - :ref:`list_software_Theano_607` - :ref:`list_software_THetA_438` - :ref:`list_software_thurstonianIRT_1454` - :ref:`list_software_TiCCutils_884` - :ref:`list_software_Tika_393` - :ref:`list_software_TiMBL_408` - :ref:`list_software_time_431` - :ref:`list_software_TINKER_461` - :ref:`list_software_TinyDB_554` - :ref:`list_software_Tk_191` - :ref:`list_software_Tkinter_737` - :ref:`list_software_TM-align_729` - :ref:`list_software_tmux_462` - :ref:`list_software_ToFu_382` - :ref:`list_software_Togl_406` - :ref:`list_software_TopHat_592` - :ref:`list_software_torchtext_997` - :ref:`list_software_torchvision_1208` - :ref:`list_software_TotalView_927` - :ref:`list_software_tqdm_438` - :ref:`list_software_Tracer_609` - :ref:`list_software_TransDecoder_1214` - :ref:`list_software_Transrate_948` - :ref:`list_software_travis_665` - :ref:`list_software_TreeMix_702` - :ref:`list_software_TreeShrink_1023` - :ref:`list_software_TRF_236` - :ref:`list_software_Triangle_822` - :ref:`list_software_Trilinos_852` - :ref:`list_software_Trim_Galore_1109` - :ref:`list_software_trimAl_617` - :ref:`list_software_Trimmomatic_1158` - :ref:`list_software_Trinity_755` - :ref:`list_software_TRIQS_403` - :ref:`list_software_TRIQS-cthyb_986` - :ref:`list_software_TRIQS-dft_tools_1422` - :ref:`list_software_TRIQS-tprf_892` - :ref:`list_software_TRUST_418` - :ref:`list_software_TurboVNC_755` - :ref:`list_software_TVB_236` - :ref:`list_software_tvb-data_787` - :ref:`list_software_TVB-deps_709` - :ref:`list_software_tvb-framework_1351` - :ref:`list_software_tvb-library_1134` .. _list_software_tabix_536: @@ -29640,6 +31533,7 @@ version toolchain ``2018_U5`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` ``2019_U4`` ``GCCcore/8.2.0`` ``2019_U9`` ``GCCcore/8.3.0`` +``2020.2`` ``GCCcore/8.3.0`` ============== ================================================== @@ -29777,9 +31671,12 @@ version versionsuffix toolchain ``1.13.1`` ``-Python-3.7.2`` ``foss/2019a``, ``fosscuda/2019a`` ``1.14.0`` ``-Python-3.7.2`` ``foss/2019a``, ``fosscuda/2019a`` ``1.15.0`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` +``1.15.2`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` ``2.0.0`` ``-Python-3.7.2`` ``foss/2019a`` ``2.0.0`` ``-Python-3.7.4`` ``fosscuda/2019b`` -``2.1.0`` ``-Python-3.7.4`` ``fosscuda/2019b`` +``2.0.1`` ``-Python-3.7.2`` ``foss/2019a`` +``2.0.1`` ``-Python-3.7.4`` ``fosscuda/2019b`` +``2.1.0`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` ========== ============================= =================================================== @@ -29929,26 +31826,27 @@ Theano is a Python library that allows you to define, optimize, and evaluate mat *homepage*: https://deeplearning.net/software/theano -========= ================== ======================================= -version versionsuffix toolchain -========= ================== ======================================= -``0.8.2`` ``-Python-2.7.11`` ``foss/2016a`` -``0.8.2`` ``-Python-3.5.1`` ``foss/2016a`` -``0.8.2`` ``-Python-3.5.2`` ``intel/2016b`` -``0.9.0`` ``-Python-2.7.13`` ``intel/2017a`` -``0.9.0`` ``-Python-3.6.1`` ``intel/2017a`` -``1.0.0`` ``-Python-2.7.14`` ``intel/2017b`` -``1.0.0`` ``-Python-3.6.3`` ``intel/2017b`` -``1.0.1`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` -``1.0.2`` ``-Python-2.7.14`` ``fosscuda/2017b``, ``intelcuda/2017b`` -``1.0.2`` ``-Python-2.7.15`` ``fosscuda/2018b`` -``1.0.2`` ``-Python-3.6.3`` ``fosscuda/2017b``, ``intelcuda/2017b`` -``1.0.2`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` -``1.0.3`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b`` -``1.0.4`` ``foss/2019a``, ``fosscuda/2019a`` -``1.0.4`` ``-Python-3.6.4`` ``foss/2018a`` -``1.0.4`` ``-Python-3.6.6`` ``fosscuda/2018b`` -========= ================== ======================================= +========= ================== =================================================== +version versionsuffix toolchain +========= ================== =================================================== +``0.8.2`` ``-Python-2.7.11`` ``foss/2016a`` +``0.8.2`` ``-Python-3.5.1`` ``foss/2016a`` +``0.8.2`` ``-Python-3.5.2`` ``intel/2016b`` +``0.9.0`` ``-Python-2.7.13`` ``intel/2017a`` +``0.9.0`` ``-Python-3.6.1`` ``intel/2017a`` +``1.0.0`` ``-Python-2.7.14`` ``intel/2017b`` +``1.0.0`` ``-Python-3.6.3`` ``intel/2017b`` +``1.0.1`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` +``1.0.2`` ``-Python-2.7.14`` ``fosscuda/2017b``, ``intelcuda/2017b`` +``1.0.2`` ``-Python-2.7.15`` ``fosscuda/2018b`` +``1.0.2`` ``-Python-3.6.3`` ``fosscuda/2017b``, ``intelcuda/2017b`` +``1.0.2`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` +``1.0.3`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b`` +``1.0.4`` ``foss/2019a``, ``fosscuda/2019a`` +``1.0.4`` ``-Python-3.6.4`` ``foss/2018a`` +``1.0.4`` ``-Python-3.6.6`` ``fosscuda/2018b`` +``1.0.4`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b`` +========= ================== =================================================== .. _list_software_THetA_438: @@ -30122,6 +32020,7 @@ version versionsuffix toolchain ``2.7.14`` ``-Python-2.7.14`` ``foss/2017b``, ``foss/2018a``, ``fosscuda/2017b``, ``intel/2017b``, ``intel/2018a``, ``intelcuda/2017b`` ``2.7.15`` ``GCCcore/8.2.0`` ``2.7.15`` ``-Python-2.7.15`` ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b`` +``2.7.16`` ``GCCcore/8.3.0`` ``3.6.1`` ``-Python-3.6.1`` ``foss/2017a``, ``intel/2017a`` ``3.6.2`` ``-Python-3.6.2`` ``foss/2017b`` ``3.6.3`` ``-Python-3.6.3`` ``foss/2017b``, ``fosscuda/2017b``, ``intel/2017b``, ``intelcuda/2017b`` @@ -30186,6 +32085,22 @@ version versionsuffix toolchain ========== ================== =============================== +.. _list_software_Togl_406: + +*Togl* +++++++ + +A Tcl/Tk widget for OpenGL rendering. + +*homepage*: https://sourceforge.net/projects/togl/ + +======= ================= +version toolchain +======= ================= +``2.0`` ``GCCcore/8.3.0`` +======= ================= + + .. _list_software_TopHat_592: *TopHat* @@ -30204,6 +32119,22 @@ version versionsuffix toolchain ========= ================== ================================================================================ +.. _list_software_torchtext_997: + +*torchtext* ++++++++++++ + +Data loaders and abstractions for text and NLP + +*homepage*: https://github.com/pytorch/text + +========= ================================ ================== +version versionsuffix toolchain +========= ================================ ================== +``0.5.0`` ``-PyTorch-1.4.0--Python-3.7.4`` ``fosscuda/2019b`` +========= ================================ ================== + + .. _list_software_torchvision_1208: *torchvision* @@ -30247,18 +32178,20 @@ version versionsuffix toolchain *tqdm* ++++++ -A fast, extensible progress bar for Python and CLI +Instantly make your loops show a smart progress meter. *homepage*: https://github.com/tqdm/tqdm -========== ================== ================= -version versionsuffix toolchain -========== ================== ================= -``4.24.0`` ``-Python-2.7.15`` ``foss/2018b`` -``4.24.0`` ``-Python-3.5.1`` ``foss/2016a`` -``4.29.0`` ``-Python-3.6.4`` ``intel/2018a`` -``4.32.1`` ``GCCcore/8.2.0`` -========== ================== ================= +========== ================== =============================== +version versionsuffix toolchain +========== ================== =============================== +``4.24.0`` ``-Python-2.7.15`` ``foss/2018b`` +``4.24.0`` ``-Python-3.5.1`` ``foss/2016a`` +``4.29.0`` ``-Python-3.6.4`` ``intel/2018a`` +``4.32.1`` ``GCCcore/8.2.0`` +``4.41.1`` ``GCCcore/8.3.0`` +``4.41.1`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` +========== ================== =============================== .. _list_software_Tracer_609: @@ -30412,25 +32345,26 @@ version versionsuffix toolchain *Trim_Galore* +++++++++++++ -Trim Galore is a wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS data. +Trim Galore is a wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS data. *homepage*: https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/ -========= ================== =============================== -version versionsuffix toolchain -========= ================== =============================== -``0.4.2`` ``foss/2016b`` -``0.4.4`` ``foss/2016b``, ``intel/2017a`` -``0.5.0`` ``foss/2018b`` -``0.5.0`` ``-Python-3.6.6`` ``intel/2018b`` -``0.6.0`` ``-Python-2.7.15`` ``foss/2018b`` -``0.6.0`` ``-Python-3.6.6`` ``foss/2018b`` -``0.6.1`` ``-Python-2.7.15`` ``foss/2018b`` -``0.6.1`` ``-Python-3.6.6`` ``foss/2018b`` -``0.6.2`` ``-Java-11`` ``GCCcore/8.2.0`` -``0.6.2`` ``-Python-2.7.15`` ``foss/2018b`` -``0.6.2`` ``-Python-3.6.6`` ``foss/2018b`` -========= ================== =============================== +========= ========================= =============================== +version versionsuffix toolchain +========= ========================= =============================== +``0.4.2`` ``foss/2016b`` +``0.4.4`` ``foss/2016b``, ``intel/2017a`` +``0.5.0`` ``foss/2018b`` +``0.5.0`` ``-Python-3.6.6`` ``intel/2018b`` +``0.6.0`` ``-Python-2.7.15`` ``foss/2018b`` +``0.6.0`` ``-Python-3.6.6`` ``foss/2018b`` +``0.6.1`` ``-Python-2.7.15`` ``foss/2018b`` +``0.6.1`` ``-Python-3.6.6`` ``foss/2018b`` +``0.6.2`` ``-Java-11`` ``GCCcore/8.2.0`` +``0.6.2`` ``-Python-2.7.15`` ``foss/2018b`` +``0.6.2`` ``-Python-3.6.6`` ``foss/2018b`` +``0.6.5`` ``-Java-11-Python-3.7.4`` ``GCCcore/8.3.0`` +========= ========================= =============================== .. _list_software_trimAl_617: @@ -30465,6 +32399,7 @@ version versionsuffix toolchain ``0.36`` ``-Java-1.8.0_92`` ``system`` ``0.38`` ``-Java-1.8`` ``system`` ``0.38`` ``-Java-1.8.0_162`` ``system`` +``0.39`` ``-Java-11`` ``system`` ======== =================== ========== @@ -30477,16 +32412,20 @@ Trinity represents a novel method for the efficient and robust de novo reconstru *homepage*: https://trinityrnaseq.github.io -========= ======================================== -version toolchain -========= ======================================== -``2.2.0`` ``foss/2016a`` -``2.4.0`` ``foss/2017a`` -``2.5.1`` ``intel/2017a``, ``intel/2017b`` -``2.6.6`` ``intel/2018a`` -``2.8.4`` ``foss/2018b`` -``2.8.5`` ``iccifort/2019.1.144-GCC-8.2.0-2.31.1`` -========= ======================================== +========== ================== ======================================== +version versionsuffix toolchain +========== ================== ======================================== +``2.2.0`` ``foss/2016a`` +``2.4.0`` ``foss/2017a`` +``2.5.1`` ``intel/2017a``, ``intel/2017b`` +``2.6.6`` ``intel/2018a`` +``2.8.4`` ``foss/2018b`` +``2.8.5`` ``iccifort/2019.1.144-GCC-8.2.0-2.31.1`` +``2.8.5`` ``-Java-11`` ``GCC/8.3.0`` +``2.9.1`` ``-Python-2.7.16`` ``foss/2019b`` +``2.9.1`` ``-Python-3.7.4`` ``foss/2019b`` +``2.10.0`` ``-Python-3.7.4`` ``foss/2019b`` +========== ================== ======================================== .. _list_software_TRIQS_403: @@ -30676,7 +32615,7 @@ version versionsuffix toolchain --- -:ref:`list_software_UCLUST_480` - :ref:`list_software_UCX_240` - :ref:`list_software_udocker_749` - :ref:`list_software_UDUNITS_556` - :ref:`list_software_UFL_231` - :ref:`list_software_UMI-tools_841` - :ref:`list_software_umis_446` - :ref:`list_software_UNAFold_617` - :ref:`list_software_Unicycler_942` - :ref:`list_software_unixODBC_732` - :ref:`list_software_unrar_552` - :ref:`list_software_UnZip_502` - :ref:`list_software_USEARCH_523` - :ref:`list_software_USPEX_405` - :ref:`list_software_utf8proc_827` - :ref:`list_software_util-linux_1051` +:ref:`list_software_UCLUST_480` - :ref:`list_software_UCX_240` - :ref:`list_software_udocker_749` - :ref:`list_software_UDUNITS_556` - :ref:`list_software_UFL_231` - :ref:`list_software_UMI-tools_841` - :ref:`list_software_umis_446` - :ref:`list_software_UNAFold_617` - :ref:`list_software_Unicycler_942` - :ref:`list_software_units_563` - :ref:`list_software_unixODBC_732` - :ref:`list_software_unrar_552` - :ref:`list_software_UnZip_502` - :ref:`list_software_UQTk_357` - :ref:`list_software_USEARCH_523` - :ref:`list_software_USPEX_405` - :ref:`list_software_utf8proc_827` - :ref:`list_software_util-linux_1051` .. _list_software_UCLUST_480: @@ -30831,6 +32770,22 @@ version versionsuffix toolchain ========= ================= ============== +.. _list_software_units_563: + +*units* ++++++++ + +GNU Units converts quantities expressed in various systems of measurement to their equivalents in other systems of measurement. Like many similar programs, it can handle multiplicative scale changes. It can also handle nonlinear conversions such as Fahrenheit to Celsius or wire gauge, and it can convert from and to sums of units, such as converting between meters and feet plus inches. + +*homepage*: https://www.gnu.org/software/units/ + +======== ================= +version toolchain +======== ================= +``2.19`` ``GCCcore/8.2.0`` +======== ================= + + .. _list_software_unixODBC_732: *unixODBC* @@ -30873,11 +32828,27 @@ UnZip is an extraction utility for archives compressed in .zip format (also call *homepage*: http://www.info-zip.org/UnZip.html -======= ======================================================= -version toolchain -======= ======================================================= -``6.0`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` -======= ======================================================= +======= ========================================================================== +version toolchain +======= ========================================================================== +``6.0`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` +======= ========================================================================== + + +.. _list_software_UQTk_357: + +*UQTk* +++++++ + +The UQ Toolkit (UQTk) is a collection of libraries and tools for the quantification of uncertainty in numerical model predictions. + +*homepage*: https://www.sandia.gov/UQToolkit/ + +========= ================= =============== +version versionsuffix toolchain +========= ================= =============== +``3.1.0`` ``-Python-3.7.4`` ``intel/2019b`` +========= ================= =============== .. _list_software_USEARCH_523: @@ -31164,6 +33135,7 @@ version versionsuffix toolchain ``0.1.15`` ``-Perl-5.24.0`` ``foss/2016b`` ``0.1.15`` ``-Perl-5.26.0`` ``foss/2017b``, ``intel/2017b`` ``0.1.15`` ``-Perl-5.26.1`` ``foss/2018a`` +``0.1.16`` ``GCC/8.3.0`` ``0.1.16`` ``-Perl-5.28.0`` ``foss/2018b``, ``intel/2018b`` ========== ================ =============================== @@ -31193,12 +33165,12 @@ Sequence assembler for very short reads *homepage*: http://www.ebi.ac.uk/~zerbino/velvet/ -========== ================ ============================== -version versionsuffix toolchain -========== ================ ============================== -``1.2.10`` ``-mt-kmer_191`` ``foss/2018a``, ``foss/2018b`` -``1.2.10`` ``-mt-kmer_37`` ``intel/2017a`` -========== ================ ============================== +========== ================ ============================================= +version versionsuffix toolchain +========== ================ ============================================= +``1.2.10`` ``-mt-kmer_191`` ``GCC/8.3.0``, ``foss/2018a``, ``foss/2018b`` +``1.2.10`` ``-mt-kmer_37`` ``intel/2017a`` +========== ================ ============================================= .. _list_software_VEP_235: @@ -31351,11 +33323,11 @@ Voro++ is a software library for carrying out three-dimensional computations of *homepage*: http://math.lbl.gov/voro++/ -========= ================================================== -version toolchain -========= ================================================== -``0.4.6`` ``GCCcore/6.4.0``, ``foss/2016a``, ``intel/2016a`` -========= ================================================== +========= =================================================================================== +version toolchain +========= =================================================================================== +``0.4.6`` ``GCCcore/6.4.0``, ``foss/2016a``, ``foss/2019b``, ``intel/2016a``, ``intel/2019b`` +========= =================================================================================== .. _list_software_vsc-base_788: @@ -31606,7 +33578,7 @@ version toolchain --- -:ref:`list_software_Wannier90_829` - :ref:`list_software_WannierTools_1253` - :ref:`list_software_wcwidth_762` - :ref:`list_software_WebKitGTK+_855` - :ref:`list_software_WebSocket++_989` - :ref:`list_software_WEKA_296` - :ref:`list_software_wget_439` - :ref:`list_software_wheel_533` - :ref:`list_software_WIEN2k_464` - :ref:`list_software_WISExome_753` - :ref:`list_software_wkhtmltopdf_1204` - :ref:`list_software_worker_666` - :ref:`list_software_WPS_250` - :ref:`list_software_WRF_239` - :ref:`list_software_WRF-Fire_674` - :ref:`list_software_wrf-python_1054` - :ref:`list_software_wxPropertyGrid_1498` - :ref:`list_software_wxPython_881` - :ref:`list_software_wxWidgets_966` +:ref:`list_software_Wannier90_829` - :ref:`list_software_WannierTools_1253` - :ref:`list_software_wcwidth_762` - :ref:`list_software_WebKitGTK+_855` - :ref:`list_software_WebSocket++_989` - :ref:`list_software_WEKA_296` - :ref:`list_software_wget_439` - :ref:`list_software_wheel_533` - :ref:`list_software_WIEN2k_464` - :ref:`list_software_WildMagic_881` - :ref:`list_software_Winnowmap_960` - :ref:`list_software_WISExome_753` - :ref:`list_software_wkhtmltopdf_1204` - :ref:`list_software_worker_666` - :ref:`list_software_WPS_250` - :ref:`list_software_WRF_239` - :ref:`list_software_WRF-Fire_674` - :ref:`list_software_wrf-python_1054` - :ref:`list_software_wxPropertyGrid_1498` - :ref:`list_software_wxPython_881` - :ref:`list_software_wxWidgets_966` .. _list_software_Wannier90_829: @@ -31722,13 +33694,13 @@ GNU Wget is a free software package for retrieving files using HTTP, HTTPS and F *homepage*: https://www.gnu.org/software/wget/ -========== ============================== -version toolchain -========== ============================== -``1.17.1`` ``foss/2016a``, ``foss/2016b`` -``1.19.4`` ``GCCcore/6.4.0`` -``1.20.1`` ``GCCcore/7.3.0`` -========== ============================== +========== ==================================== +version toolchain +========== ==================================== +``1.17.1`` ``foss/2016a``, ``foss/2016b`` +``1.19.4`` ``GCCcore/6.4.0`` +``1.20.1`` ``GCCcore/7.3.0``, ``GCCcore/8.3.0`` +========== ==================================== .. _list_software_wheel_533: @@ -31773,6 +33745,38 @@ version toolchain ======== ================================================ +.. _list_software_WildMagic_881: + +*WildMagic* ++++++++++++ + +Wild Magic 5.17 + +*homepage*: https://www.geometrictools.com/index.html + +======== ============== +version toolchain +======== ============== +``5.17`` ``foss/2018b`` +======== ============== + + +.. _list_software_Winnowmap_960: + +*Winnowmap* ++++++++++++ + +Winnowmap is a long-read mapping algorithm, and a result of our exploration into superior minimizer sampling techniques. + +*homepage*: https://github.com/marbl/Winnowmap + +======= ============= +version toolchain +======= ============= +``1.0`` ``GCC/8.3.0`` +======= ============= + + .. _list_software_WISExome_753: *WISExome* @@ -31961,7 +33965,7 @@ version toolchain --- -:ref:`list_software_X11_186` - :ref:`list_software_x264_276` - :ref:`list_software_x265_277` - :ref:`list_software_xarray_663` - :ref:`list_software_xbitmaps_872` - :ref:`list_software_xcb-proto_926` - :ref:`list_software_xcb-util_808` - :ref:`list_software_xcb-util-image_1368` - :ref:`list_software_xcb-util-keysyms_1642` - :ref:`list_software_xcb-util-renderutil_1939` - :ref:`list_software_xcb-util-wm_1081` - :ref:`list_software_xCell_504` - :ref:`list_software_XCfun_484` - :ref:`list_software_XCrySDen_752` - :ref:`list_software_Xerces-C++_816` - :ref:`list_software_xextproto_1021` - :ref:`list_software_xf86vidmodeproto_1640` - :ref:`list_software_XGBoost_678` - :ref:`list_software_xineramaproto_1417` - :ref:`list_software_XKeyboardConfig_1503` - :ref:`list_software_XMDS2_366` - :ref:`list_software_Xmipp_526` - :ref:`list_software_XML-LibXML_806` - :ref:`list_software_XML-Parser_907` - :ref:`list_software_xmlf90_544` - :ref:`list_software_XMLSec_524` - :ref:`list_software_XMLStarlet_976` - :ref:`list_software_xonsh_560` - :ref:`list_software_xorg-macros_1138` - :ref:`list_software_xprop_569` - :ref:`list_software_xproto_684` - :ref:`list_software_XSD_239` - :ref:`list_software_XTandem_689` - :ref:`list_software_xtrans_672` - :ref:`list_software_XZ_178` +:ref:`list_software_X11_186` - :ref:`list_software_x264_276` - :ref:`list_software_x265_277` - :ref:`list_software_xarray_663` - :ref:`list_software_xbitmaps_872` - :ref:`list_software_xcb-proto_926` - :ref:`list_software_xcb-util_808` - :ref:`list_software_xcb-util-image_1368` - :ref:`list_software_xcb-util-keysyms_1642` - :ref:`list_software_xcb-util-renderutil_1939` - :ref:`list_software_xcb-util-wm_1081` - :ref:`list_software_xCell_504` - :ref:`list_software_XCfun_484` - :ref:`list_software_XCrySDen_752` - :ref:`list_software_Xerces-C++_816` - :ref:`list_software_xextproto_1021` - :ref:`list_software_xf86vidmodeproto_1640` - :ref:`list_software_XGBoost_678` - :ref:`list_software_xineramaproto_1417` - :ref:`list_software_XKeyboardConfig_1503` - :ref:`list_software_XMDS2_366` - :ref:`list_software_Xmipp_526` - :ref:`list_software_XML-LibXML_806` - :ref:`list_software_XML-Parser_907` - :ref:`list_software_xmlf90_544` - :ref:`list_software_XMLSec_524` - :ref:`list_software_XMLStarlet_976` - :ref:`list_software_xonsh_560` - :ref:`list_software_xorg-macros_1138` - :ref:`list_software_xprop_569` - :ref:`list_software_xproto_684` - :ref:`list_software_XSD_239` - :ref:`list_software_XTandem_689` - :ref:`list_software_xtb_334` - :ref:`list_software_xtrans_672` - :ref:`list_software_XZ_178` .. _list_software_X11_186: @@ -32045,20 +34049,21 @@ xarray (formerly xray) is an open source project and Python package that aims to *homepage*: https://github.com/pydata/xarray -========== ================== =============== -version versionsuffix toolchain -========== ================== =============== -``0.9.5`` ``-Python-2.7.13`` ``intel/2017a`` -``0.9.5`` ``-Python-3.6.1`` ``intel/2017a`` -``0.9.6`` ``-Python-2.7.13`` ``intel/2017a`` -``0.10.0`` ``-Python-2.7.14`` ``intel/2017b`` -``0.10.0`` ``-Python-3.6.3`` ``intel/2017b`` -``0.10.3`` ``-Python-3.6.4`` ``intel/2018a`` -``0.10.4`` ``-Python-3.6.4`` ``intel/2018a`` -``0.10.8`` ``-Python-3.6.4`` ``intel/2018a`` -``0.12.1`` ``-Python-3.6.6`` ``intel/2018b`` -``0.13.0`` ``-Python-3.7.2`` ``intel/2019a`` -========== ================== =============== +========== ================== =============================== +version versionsuffix toolchain +========== ================== =============================== +``0.9.5`` ``-Python-2.7.13`` ``intel/2017a`` +``0.9.5`` ``-Python-3.6.1`` ``intel/2017a`` +``0.9.6`` ``-Python-2.7.13`` ``intel/2017a`` +``0.10.0`` ``-Python-2.7.14`` ``intel/2017b`` +``0.10.0`` ``-Python-3.6.3`` ``intel/2017b`` +``0.10.3`` ``-Python-3.6.4`` ``intel/2018a`` +``0.10.4`` ``-Python-3.6.4`` ``intel/2018a`` +``0.10.8`` ``-Python-3.6.4`` ``intel/2018a`` +``0.12.1`` ``-Python-3.6.6`` ``intel/2018b`` +``0.13.0`` ``-Python-3.7.2`` ``intel/2019a`` +``0.15.1`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` +========== ================== =============================== .. _list_software_xbitmaps_872: @@ -32216,11 +34221,12 @@ XCrySDen is a crystalline and molecular structure visualisation program aiming *homepage*: http://www.xcrysden.org/ -========== =============== -version toolchain -========== =============== -``1.5.60`` ``intel/2019a`` -========== =============== +========== =============================== +version toolchain +========== =============================== +``1.5.60`` ``intel/2019a`` +``1.6.2`` ``foss/2019b``, ``intel/2019b`` +========== =============================== .. _list_software_Xerces-C++_816: @@ -32289,6 +34295,7 @@ version versionsuffix toolchain ``0.6a2`` ``-Python-3.5.2`` ``intel/2016b`` ``0.6a2`` ``-Python-3.6.1`` ``intel/2017a`` ``0.72.1`` ``-Python-2.7.14`` ``intel/2017b`` +``0.90`` ``-Python-3.7.4`` ``foss/2019b`` ``20171120`` ``-Java-1.8.0_152`` ``intel/2017b`` ============ =================== =============== @@ -32414,6 +34421,7 @@ xmlf90 is a basic XML parsing library written in Fortran. version toolchain ========= ============================== ``1.5.3`` ``foss/2016b``, ``foss/2017a`` +``1.5.4`` ``iccifort/2019.5.281`` ========= ============================== @@ -32552,6 +34560,23 @@ version toolchain ============== ========================================================== +.. _list_software_xtb_334: + +*xtb* ++++++ + +xtb - An extended tight-binding semi-empirical program package. + +*homepage*: https://xtb-docs.readthedocs.io + +================ ================= =============== +version versionsuffix toolchain +================ ================= =============== +``6.2.2-hotfix`` ``-Python-3.6.3`` ``intel/2017b`` +``6.2.3`` ``foss/2019b`` +================ ================= =============== + + .. _list_software_xtrans_672: *xtrans* @@ -32638,7 +34663,7 @@ version versionsuffix toolchain ``1.5.0`` ``-Python-2.7.15`` ``intel/2018b`` ``1.5.0`` ``-Python-3.7.2`` ``intel/2019a`` ``1.6.0`` ``-Python-3.7.2`` ``intel/2019a`` -``1.6.0`` ``-Python-3.7.4`` ``intel/2019b`` +``1.6.0`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` ==================== ============================== ================================================ @@ -32715,7 +34740,7 @@ version toolchain --- -:ref:`list_software_zarr_447` - :ref:`list_software_ZeroMQ_574` - :ref:`list_software_zingeR_623` - :ref:`list_software_zlib_433` - :ref:`list_software_zlibbioc_846` - :ref:`list_software_ZPAQ_316` - :ref:`list_software_zsh_341` - :ref:`list_software_zstd_453` +:ref:`list_software_zarr_447` - :ref:`list_software_ZeroMQ_574` - :ref:`list_software_zingeR_623` - :ref:`list_software_Zip_307` - :ref:`list_software_zlib_433` - :ref:`list_software_zlibbioc_846` - :ref:`list_software_ZPAQ_316` - :ref:`list_software_zsh_341` - :ref:`list_software_zstd_453` .. _list_software_zarr_447: @@ -32771,6 +34796,22 @@ version versionsuffix toolchain ============ ============= ============== +.. _list_software_Zip_307: + +*Zip* ++++++ + +Zip is a compression and file packaging/archive utility. Although highly compatible both with PKWARE's PKZIP and PKUNZIP utilities for MS-DOS and with Info-ZIP's own UnZip, our primary objectives have been portability and other-than-MSDOS functionality + +*homepage*: http://www.info-zip.org/Zip.html + +======= ==================================== +version toolchain +======= ==================================== +``3.0`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` +======= ==================================== + + .. _list_software_zlib_433: *zlib* @@ -32786,7 +34827,7 @@ version toolchain ``1.2.7`` ``GCC/4.8.1``, ``GCC/4.8.2`` ``1.2.8`` ``GCC/4.8.2``, ``GCC/4.8.3``, ``GCC/4.8.4``, ``GCC/4.9.2``, ``GCC/4.9.2-binutils-2.25``, ``GCC/4.9.3``, ``GCC/4.9.3-2.25``, ``GCC/4.9.3-binutils-2.25``, ``GCC/5.1.0-binutils-2.25``, ``GCCcore/4.9.2``, ``GCCcore/4.9.3``, ``GCCcore/4.9.4``, ``GCCcore/5.3.0``, ``GCCcore/5.4.0``, ``GCCcore/6.1.0``, ``GCCcore/6.2.0``, ``GCCcore/6.3.0``, ``GNU/4.9.3-2.25``, ``foss/2016.04``, ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016.02-GCC-4.9``, ``intel/2016a``, ``intel/2016b``, ``intel/2017.01``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25``, ``system`` ``1.2.10`` ``system`` -``1.2.11`` ``GCCcore/5.4.0``, ``GCCcore/5.5.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.1.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/7.4.0``, ``GCCcore/8.1.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.1.0``, ``GCCcore/9.2.0``, ``GCCcore/system``, ``gimkl/2017a``, ``system`` +``1.2.11`` ``GCCcore/5.4.0``, ``GCCcore/5.5.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.1.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/7.4.0``, ``GCCcore/8.1.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.1.0``, ``GCCcore/9.2.0``, ``GCCcore/9.3.0``, ``GCCcore/system``, ``gimkl/2017a``, ``system`` ========== ===================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== diff --git a/docs/version-specific/easyblocks.rst b/docs/version-specific/easyblocks.rst index 6325e2d8..6505e118 100644 --- a/docs/version-specific/easyblocks.rst +++ b/docs/version-specific/easyblocks.rst @@ -69,9 +69,11 @@ * EB_DIRAC * EB_Doxygen * EB_Eigen + * EB_ELSI * EB_GATE * EB_Geant4 * EB_GROMACS + * EB_LAMMPS * EB_netCDF * EB_OpenBabel * EB_OpenCV @@ -84,6 +86,7 @@ * EB_Amber * EB_ARB * EB_ATLAS + * EB_BerkeleyGW * EB_binutils * EB_BLACS * EB_Bowtie @@ -91,6 +94,7 @@ * EB_bzip2 * EB_CBLAS * EB_Chapel + * EB_CMake * EB_cppcheck * EB_Cufflinks * EB_DB @@ -119,6 +123,7 @@ * EB_HPL * EB_Hypre * EB_LAPACK + * EB_libdrm * EB_Libint * EB_libQGLViewer * EB_libxml2 @@ -251,6 +256,7 @@ * EB_PyQuante * EB_python_minus_meep * EB_PyZMQ + * EB_SEPP * EB_TensorFlow * EB_TensorRT * EB_VSC_minus_tools @@ -308,6 +314,7 @@ * MesonNinja * CMakeNinja + * EB_Mesa * ModuleRC * PackedBinary @@ -372,6 +379,7 @@ * EB_PyQuante * EB_python_minus_meep * EB_PyZMQ + * EB_SEPP * EB_TensorFlow * EB_TensorRT * EB_VSC_minus_tools diff --git a/docs/version-specific/easyconfig_templates.rst b/docs/version-specific/easyconfig_templates.rst index c41fee53..b838bfe3 100644 --- a/docs/version-specific/easyconfig_templates.rst +++ b/docs/version-specific/easyconfig_templates.rst @@ -24,6 +24,8 @@ Template names/values for (short) software versions ==================== ========================================== Template name Template value ==================== ========================================== +``%(cudashortver)s`` short version for CUDA (.) +``%(cudaver)s`` full version for CUDA ``%(javashortver)s`` short version for Java (.) ``%(javaver)s`` full version for Java ``%(perlshortver)s`` short version for Perl (.) diff --git a/docs/version-specific/generic_easyblocks.rst b/docs/version-specific/generic_easyblocks.rst index 19d45027..478218ec 100644 --- a/docs/version-specific/generic_easyblocks.rst +++ b/docs/version-specific/generic_easyblocks.rst @@ -173,13 +173,14 @@ easyconfig parameter description ``abs_path_compilers`` Specify compilers via absolute file path (not via command names) ``False`` ``allow_system_boost`` Always allow CMake to pick up on Boost installed in OS (even if Boost is included as a dependency) ``False`` ``build_cmd`` Build command to use ``"make"`` -``build_type`` Build type for CMake, e.g. Release or Debug.Use None to not specify -DCMAKE_BUILD_TYPE ``None`` +``build_shared_libs`` Build shared library (instead of static library)None can be used to add no flag (usually results in static library) ``None`` +``build_type`` Build type for CMake, e.g. Release.Defaults to 'Release' or 'Debug' depending on toolchainopts[debug] ``None`` ``configure_cmd`` Configure command to use ``"cmake"`` ``configure_cmd_prefix`` Prefix to be glued before ./configure ``""`` ``host_type`` Value to provide to --host option of configure script, e.g., x86_64-pc-linux-gnu (determined by config.guess shipped with EasyBuild if None, False implies to leave it up to the configure script) ``None`` ``install_cmd`` Build command to use ``"make install"`` ``prefix_opt`` Prefix command line option for configure script ('--prefix=' if None) ``None`` -``separate_build_dir`` Perform build in a separate directory ``False`` +``separate_build_dir`` Perform build in a separate directory ``True`` ``srcdir`` Source directory location to provide to cmake command ``None`` ``tar_config_opts`` Override tar settings as determined by configure. ``False`` ======================== ================================================================================================================================================================================================== ================== @@ -246,14 +247,15 @@ easyconfig parameter description ``abs_path_compilers`` Specify compilers via absolute file path (not via command names) ``False`` ``allow_system_boost`` Always allow CMake to pick up on Boost installed in OS (even if Boost is included as a dependency) ``False`` ``build_cmd`` Build command to use ``"make"`` -``build_type`` Build type for CMake, e.g. Release or Debug.Use None to not specify -DCMAKE_BUILD_TYPE ``None`` +``build_shared_libs`` Build shared library (instead of static library)None can be used to add no flag (usually results in static library) ``None`` +``build_type`` Build type for CMake, e.g. Release.Defaults to 'Release' or 'Debug' depending on toolchainopts[debug] ``None`` ``configure_cmd`` Configure command to use ``"cmake"`` ``configure_cmd_prefix`` Prefix to be glued before ./configure ``""`` ``files_to_copy`` List of files or dirs to copy ``None`` ``host_type`` Value to provide to --host option of configure script, e.g., x86_64-pc-linux-gnu (determined by config.guess shipped with EasyBuild if None, False implies to leave it up to the configure script) ``None`` ``install_cmd`` Build command to use ``"make install"`` ``prefix_opt`` Prefix command line option for configure script ('--prefix=' if None) ``None`` -``separate_build_dir`` Perform build in a separate directory ``False`` +``separate_build_dir`` Perform build in a separate directory ``True`` ``srcdir`` Source directory location to provide to cmake command ``None`` ``tar_config_opts`` Override tar settings as determined by configure. ``False`` ``with_configure`` Run configure script before building ``False`` @@ -282,13 +284,14 @@ easyconfig parameter description ``abs_path_compilers`` Specify compilers via absolute file path (not via command names) ``False`` ``allow_system_boost`` Always allow CMake to pick up on Boost installed in OS (even if Boost is included as a dependency) ``False`` ``build_cmd`` Build command to use ``"make"`` -``build_type`` Build type for CMake, e.g. Release or Debug.Use None to not specify -DCMAKE_BUILD_TYPE ``None`` +``build_shared_libs`` Build shared library (instead of static library)None can be used to add no flag (usually results in static library) ``None`` +``build_type`` Build type for CMake, e.g. Release.Defaults to 'Release' or 'Debug' depending on toolchainopts[debug] ``None`` ``configure_cmd`` Configure command to use ``"cmake"`` ``configure_cmd_prefix`` Prefix to be glued before ./configure ``""`` ``host_type`` Value to provide to --host option of configure script, e.g., x86_64-pc-linux-gnu (determined by config.guess shipped with EasyBuild if None, False implies to leave it up to the configure script) ``None`` ``install_cmd`` Build command to use ``"make install"`` ``prefix_opt`` Prefix command line option for configure script ('--prefix=' if None) ``None`` -``separate_build_dir`` Perform build in a separate directory ``False`` +``separate_build_dir`` Perform build in a separate directory ``True`` ``srcdir`` Source directory location to provide to cmake command ``None`` ``tar_config_opts`` Override tar settings as determined by configure. ``False`` ======================== ================================================================================================================================================================================================== ================== @@ -325,7 +328,8 @@ easyconfig parameter description ``abs_path_compilers`` Specify compilers via absolute file path (not via command names) ``False`` ``allow_system_boost`` Always allow CMake to pick up on Boost installed in OS (even if Boost is included as a dependency) ``False`` ``build_cmd`` Build command to use ``"make"`` -``build_type`` Build type for CMake, e.g. Release or Debug.Use None to not specify -DCMAKE_BUILD_TYPE ``None`` +``build_shared_libs`` Build shared library (instead of static library)None can be used to add no flag (usually results in static library) ``None`` +``build_type`` Build type for CMake, e.g. Release.Defaults to 'Release' or 'Debug' depending on toolchainopts[debug] ``None`` ``buildcmd`` Command to pass to setup.py to build the extension ``"build"`` ``check_ldshared`` Check Python value of $LDSHARED, correct if needed to "$CC -shared" ``None`` ``configure_cmd`` Configure command to use ``"cmake"`` @@ -341,13 +345,14 @@ easyconfig parameter description ``req_py_minver`` Required minor Python version (only relevant when using system Python) ``None`` ``runtest`` Run unit tests. ``True`` ``sanity_pip_check`` Run 'pip check' to ensure all required Python packages are installed ``False`` -``separate_build_dir`` Perform build in a separate directory ``False`` +``separate_build_dir`` Perform build in a separate directory ``True`` ``srcdir`` Source directory location to provide to cmake command ``None`` ``tar_config_opts`` Override tar settings as determined by configure. ``False`` ``unpack_sources`` Unpack sources prior to build/install ``True`` ``use_easy_install`` Install using '%(python)s setup.py easy_install --prefix=%(prefix)s %(installopts)s %(loc)s' (deprecated) ``False`` ``use_pip`` Install using 'pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``None`` ``use_pip_editable`` Install using 'pip install --editable' ``False`` +``use_pip_extras`` String with comma-separated list of 'extras' to install via pip ``None`` ``use_pip_for_deps`` Install dependencies using 'pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``False`` ``use_setup_py_develop`` Install using '%(python)s setup.py develop --prefix=%(prefix)s %(installopts)s' (deprecated) ``False`` ``zipped_egg`` Install as a zipped eggs (requires use_easy_install) ``False`` @@ -537,6 +542,7 @@ easyconfig parameter description ``use_easy_install`` Install using '%(python)s setup.py easy_install --prefix=%(prefix)s %(installopts)s %(loc)s' (deprecated) ``False`` ``use_pip`` Install using 'pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``None`` ``use_pip_editable`` Install using 'pip install --editable' ``False`` +``use_pip_extras`` String with comma-separated list of 'extras' to install via pip ``None`` ``use_pip_for_deps`` Install dependencies using 'pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``False`` ``use_setup_py_develop`` Install using '%(python)s setup.py develop --prefix=%(prefix)s %(installopts)s' (deprecated) ``False`` ``zipped_egg`` Install as a zipped eggs (requires use_easy_install) ``False`` @@ -635,6 +641,7 @@ easyconfig parameter description ``use_easy_install`` Install using '%(python)s setup.py easy_install --prefix=%(prefix)s %(installopts)s %(loc)s' (deprecated) ``False`` ``use_pip`` Install using 'pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``None`` ``use_pip_editable`` Install using 'pip install --editable' ``False`` +``use_pip_extras`` String with comma-separated list of 'extras' to install via pip ``None`` ``use_pip_for_deps`` Install dependencies using 'pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``False`` ``use_setup_py_develop`` Install using '%(python)s setup.py develop --prefix=%(prefix)s %(installopts)s' (deprecated) ``False`` ``zipped_egg`` Install as a zipped eggs (requires use_easy_install) ``False`` @@ -904,6 +911,7 @@ easyconfig parameter description ``use_easy_install`` Install using '%(python)s setup.py easy_install --prefix=%(prefix)s %(installopts)s %(loc)s' (deprecated) ``False`` ``use_pip`` Install using 'pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``None`` ``use_pip_editable`` Install using 'pip install --editable' ``False`` +``use_pip_extras`` String with comma-separated list of 'extras' to install via pip ``None`` ``use_pip_for_deps`` Install dependencies using 'pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``False`` ``use_setup_py_develop`` Install using '%(python)s setup.py develop --prefix=%(prefix)s %(installopts)s' (deprecated) ``False`` ``zipped_egg`` Install as a zipped eggs (requires use_easy_install) ``False`` @@ -938,6 +946,7 @@ easyconfig parameter description ``use_easy_install`` Install using '%(python)s setup.py easy_install --prefix=%(prefix)s %(installopts)s %(loc)s' (deprecated) ``False`` ``use_pip`` Install using 'pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``None`` ``use_pip_editable`` Install using 'pip install --editable' ``False`` +``use_pip_extras`` String with comma-separated list of 'extras' to install via pip ``None`` ``use_pip_for_deps`` Install dependencies using 'pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``False`` ``use_setup_py_develop`` Install using '%(python)s setup.py develop --prefix=%(prefix)s %(installopts)s' (deprecated) ``False`` ``zipped_egg`` Install as a zipped eggs (requires use_easy_install) ``False`` @@ -1225,6 +1234,7 @@ easyconfig parameter description ``use_easy_install`` Install using '%(python)s setup.py easy_install --prefix=%(prefix)s %(installopts)s %(loc)s' (deprecated) ``False`` ``use_pip`` Install using 'pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``None`` ``use_pip_editable`` Install using 'pip install --editable' ``False`` +``use_pip_extras`` String with comma-separated list of 'extras' to install via pip ``None`` ``use_pip_for_deps`` Install dependencies using 'pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``False`` ``use_setup_py_develop`` Install using '%(python)s setup.py develop --prefix=%(prefix)s %(installopts)s' (deprecated) ``False`` ``zipped_egg`` Install as a zipped eggs (requires use_easy_install) ``False`` @@ -1259,6 +1269,7 @@ easyconfig parameter description ``use_easy_install`` Install using '%(python)s setup.py easy_install --prefix=%(prefix)s %(installopts)s %(loc)s' (deprecated) ``False`` ``use_pip`` Install using 'pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``None`` ``use_pip_editable`` Install using 'pip install --editable' ``False`` +``use_pip_extras`` String with comma-separated list of 'extras' to install via pip ``None`` ``use_pip_for_deps`` Install dependencies using 'pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``False`` ``use_setup_py_develop`` Install using '%(python)s setup.py develop --prefix=%(prefix)s %(installopts)s' (deprecated) ``False`` ``zipped_egg`` Install as a zipped eggs (requires use_easy_install) ``False`` diff --git a/docs/version-specific/help.rst b/docs/version-specific/help.rst index d7075cdb..0af240bb 100644 --- a/docs/version-specific/help.rst +++ b/docs/version-specific/help.rst @@ -58,7 +58,9 @@ Option flag Option description ``-x, --extended-dry-run`` Print build environment and (expected) build procedure that will be performed (default: False) ``--extended-dry-run-ignore-errors`` Ignore errors that occur during dry run (default: True; disable with --disable-extended-dry-run-ignore-errors) ``-f, --force`` Force to rebuild software even if it's already installed (i.e. if it can be found as module), and skipping check for OS dependencies (default: False) +``--ignore-locks`` Ignore locks that prevent two identical installations running in parallel (default: False) ``--job`` Submit the build as a job (default: False) +``--locks-dir=LOCKS-DIR`` Directory to store lock files (should be on a shared filesystem); None implies .locks subdirectory of software installation directory ``-l, --logtostdout`` Redirect main log to stdout (default: False) ``-M, --missing-modules`` Print list of missing modules for dependencies of specified easyconfigs (default: False) ``-b BLOCKS, --only-blocks=BLOCKS`` Only build listed blocks (type comma-separated list) @@ -105,7 +107,7 @@ Option flag Option desc ``--packagepath=PACKAGEPATH`` The destination path for the packages built by package-tool (default: /home/example/.local/easybuild/packages) ``--prefix=PREFIX`` Change prefix for buildpath, installpath, sourcepath and repositorypath (used prefix for defaults /home/example/.local/easybuild) ``--recursive-module-unload`` Enable generating of modules that unload recursively. (default: False) -``--repository=REPOSITORY`` Repository type, using repositorypath (type choice; default: FileRepository) (choices: FileRepository, GitRepository, HgRepository) +``--repository=REPOSITORY`` Repository type, using repositorypath (type choice; default: FileRepository) (choices: FileRepository, GitRepository) ``--repositorypath=REPOSITORYPATH`` Repository path, used by repository (is passed as list of arguments to create the repository instance). For more info, use --avail-repositories. (type comma-separated list; default: /home/example/.local/easybuild/ebfiles_repo) ``--sourcepath=SOURCEPATH`` Path(s) to where sources should be downloaded (string, colon-separated) (default: /home/example/.local/easybuild/sources) ``--subdir-modules=SUBDIR-MODULES`` Installpath subdir for modules (default: modules) @@ -138,7 +140,10 @@ Options for Easyconfigs =================================================== ===================================================================================================================================================================================================================================================== Option flag Option description =================================================== ===================================================================================================================================================================================================================================================== +``--create-index=CREATE-INDEX`` Create index for files in specified directory ``--fix-deprecated-easyconfigs`` Fix use of deprecated functionality in specified easyconfig files. (default: False) +``--ignore-index`` Ignore index when searching for files (default: False) +``--index-max-age=INDEX-MAX-AGE`` Maximum age for index before it is considered stale (in seconds) (type ; default: 604800) ``--inject-checksums=INJECT-CHECKSUMS`` Inject checksums of specified type for sources/patches into easyconfig file(s) (type choice; default: sha256) (choices: adler32, crc32, md5, sha1, sha256, sha512, size) ``--local-var-naming-check=LOCAL-VAR-NAMING-CHECK`` Mode to use when checking whether local variables follow the recommended naming scheme ('log': only log warnings (no printed messages); 'warn': print warnings; 'error': fail with an error) (type choice; default: warn) (choices: error, log, warn) =================================================== ===================================================================================================================================================================================================================================================== @@ -161,6 +166,7 @@ Option flag Option description ``--git-working-dirs-path=GIT-WORKING-DIRS-PATH`` Path to Git working directories for EasyBuild repositories (type ) ``--github-org=GITHUB-ORG`` GitHub organization (type ) ``--github-user=GITHUB-USER`` GitHub username (type ) +``--include-easyblocks-from-pr=PR#`` Include easyblocks from specified PR (type ) ``--install-github-token`` Install GitHub token (requires --github-user) (default: False) ``--list-prs=STATE,ORDER,DIRECTION`` List pull requests (type ; default: open,created,desc) ``--merge-pr=PR#`` Merge pull request (type ) @@ -172,7 +178,7 @@ Option flag Option description ``--pr-descr=PR-DESCR`` Description for new pull request created with --new-pr (type ) ``--pr-target-account=PR-TARGET-ACCOUNT`` Target account for new PRs (type ; default: easybuilders) ``--pr-target-branch=PR-TARGET-BRANCH`` Target branch for new PRs (type ; default: develop) -``--pr-target-repo=PR-TARGET-REPO`` Target repository for new/updating PRs (type ; default: easybuild-easyconfigs) +``--pr-target-repo=PR-TARGET-REPO`` Target repository for new/updating PRs (default: auto-detect based on provided files) (type ) ``--pr-title=PR-TITLE`` Title for new pull request created with --new-pr (type ) ``--preview-pr`` Preview a new pull request (default: False) ``--review-pr=PR#`` Review specified pull request (type ) @@ -305,6 +311,7 @@ Option flag Opt ``--use-existing-modules`` Use existing modules when resolving dependencies with minimal toolchains (default: False) ``--use-f90cache=PATH`` Enable use of f90cache to speed up compilation, with specified cache dir (type ; default: False) ``--verify-easyconfig-filenames`` Verify whether filename of specified easyconfigs matches with contents (default: False) +``--wait-on-lock=WAIT-ON-LOCK`` Wait interval (in seconds) to use when waiting for existing lock to be removed (0: implies no waiting, but exiting with an error) (type ; default: 0) ``--zip-logs=ZIP-LOGS`` Zip logs that are copied to install directory, using specified command (default: gzip) ========================================================================= ================================================================================================================================================================================== @@ -354,6 +361,7 @@ Option flag Option description ``--try-toolchain=NAME,VERSION`` Try to search and build with given toolchain (name and version) (USE WITH CARE!) (type comma-separated list) ``--try-toolchain-name=NAME`` Try to search and build with given toolchain name (USE WITH CARE!) ``--try-toolchain-version=VERSION`` Try to search and build with given toolchain version (USE WITH CARE!) +``--try-update-deps`` Try to update versions of the dependencies of an easyconfig based on what is available in the robot path (default: False) =================================== =================================================================================================================================================================== diff --git a/setup.py b/setup.py index 92eb5c04..cb2ece20 100644 --- a/setup.py +++ b/setup.py @@ -36,7 +36,13 @@ # note: release candidates should be versioned as a pre-release, e.g. "1.1rc1" # 1.1-rc1 would indicate a post-release, i.e., and update of 1.1, so beware -VERSION = '4.1.2' + +# note: using '4.2.0.post0' as version for EasyBuild v4.2.0 because of +# mistake in easybuild-4.2.0 package that was pushed to PyPI; +# the version of easyblocks/easyconfigs was accidentally still locked to '==4.1.1', +# see https://github.com/easybuilders/easybuild/pull/615/commits/3a8c81b1baaff93d3dc94b9b0cadc9bdf43d8fae +PYPI_VERSION = '4.2.0.post0' +VERSION = '4.2.0' # Utility function to read README file @@ -51,7 +57,7 @@ def read(fname): setup( name="easybuild", - version=str(VERSION), + version=PYPI_VERSION, author="EasyBuild community", author_email="easybuild@lists.ugent.be", description="""EasyBuild is a software build \ @@ -81,17 +87,13 @@ def read(fname): # for distutils requires=[ 'easybuild_framework(==%s)' % VERSION, - # there is no 4.1.2 release for easyblocks/easyconfigs, - # only for framework (which includes an important security-related bug fix) - 'easybuild_easyblocks(==4.1.1)', - 'easybuild_easyconfigs(==4.1.1)', + 'easybuild_easyblocks(==%s)' % VERSION, + 'easybuild_easyconfigs(==%s)' % VERSION, ], # for setuptools/pip install_requires=[ 'easybuild-framework == %s' % VERSION, - # there is no 4.1.2 release for easyblocks/easyconfigs, - # only for framework (which includes an important security-related bug fix) - 'easybuild-easyblocks == 4.1.1', - 'easybuild-easyconfigs == 4.1.1' + 'easybuild-easyblocks == %s' % VERSION, + 'easybuild-easyconfigs == %s' % VERSION, ], )