diff --git a/.travis.yml b/.travis.yml index 9de86320..a330ae7b 100644 --- a/.travis.yml +++ b/.travis.yml @@ -1,11 +1,12 @@ language: python -matrix: +jobs: include: - python: "2.7" - python: "3.6" + - python: "3.8" # command to install dependencies install: - - pip install sphinx codespell + - pip install codespell flake8 sphinx # command to run tests script: # it is (currently) impossible to dismiss ignored suggestions but these are @@ -13,6 +14,7 @@ script: # suggestions). Since we know we have one of these, we allow for that. # see https://github.com/easybuilders/easybuild/pull/485 for details - codespell --skip=".git,version-specific,scripts" --ignore-words-list=atleast,ninjs,simpy,proovread --quiet-level=2; retVal=$?; if [ $retVal -eq 1 ]; then echo "Got one expected warning, so success!"; else $(exit $retVal); fi; + - flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics - READTHEDOCS=1 sphinx-build docs build # test installation too (using options that don't require to have a modules tool installed) - pip install $TRAVIS_BUILD_DIR diff --git a/docs/Changelog.rst b/docs/Changelog.rst index 97cf28f6..50e67e0c 100644 --- a/docs/Changelog.rst +++ b/docs/Changelog.rst @@ -5,6 +5,7 @@ Changelog for EasyBuild documentation (for EasyBuild release notes, see :ref:`release_notes`) +* **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`) * **release 20191015.01** (`Oct 15th 2019`): update release notes for EasyBuild v4.0.1 (see :ref:`release_notes_eb401`) * **release 20190920.01** (`Sep 20th 2019`): update release notes for EasyBuild v4.0.0 (see :ref:`release_notes_eb400`); see also :ref:`eb4_changes_overview` diff --git a/docs/Python-2-3-compatibility.rst b/docs/Python-2-3-compatibility.rst index c4cbeae1..6fe69a40 100644 --- a/docs/Python-2-3-compatibility.rst +++ b/docs/Python-2-3-compatibility.rst @@ -11,6 +11,7 @@ More specifically, the following Python versions are currently supported: * Python 3.5.x * Python 3.6.x * Python 3.7.x +* Python 3.8.x (requires EasyBuild v4.1.0) .. _py2_py3_compatibility_EB_VERBOSE: diff --git a/docs/Release_notes.rst b/docs/Release_notes.rst index d4b180e2..425d5776 100644 --- a/docs/Release_notes.rst +++ b/docs/Release_notes.rst @@ -3,12 +3,178 @@ EasyBuild release notes ======================= -The latest version of EasyBuild provides support for building and installing **1,771** different software packages, -including 31 different (compiler) toolchains. It contains 211 software-specific easyblocks and 36 generic easyblocks, -alongside 8,748 easyconfig files. +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. .. note:: See also the :ref:`concise overview of major changes in EasyBuild v4.0 `. +.. _release_notes_eb411: + +EasyBuild v4.1.1 (January 16th 2020) +------------------------------------ + +bugfix/update release + +**framework** + +* various enhancements, including: + + * add ``check_log_for_errors`` function (in ``easybuild.tools.run``) to detect and handle multiple errors (`#3118 `_) + * implement support for ``eb --show-ec`` to show contents of specified easyconfig file (`#3132 `_) + * also update ``$XDG_DATA_DIR`` (share/) and ``$GI_TYPELIB_PATH`` environment variables (lib*/girepository-*) in generated module files (`#3133 `_) + * add support for ``--copy-ec`` to copy easyconfig file to specified location (`#3142 `_) + * mention ``--disable-*`` option in ``--help`` output for boolean options enabled by default (`#3151 `_) + * add ``--cuda-compute-capabilities`` configuration option (`#3161 `_) + +* various bug fixes, including: + + * ignore imports from ``vsc`` namespace made from pkgutil.py (`#3120 `_) + * only actually change permissions using ``os.chmod`` in ``adjust_permissions`` if the current permissions are not correct already (`#3125 `_) + * use ``shutil.copyfile`` to just copy file contents if target path exists and is owned by someone else (`#3127 `_) + * fix or avoid warnings that commonly arise in build log (`#3129 `_) + * disable buffering in ``asyncprocess.Popen`` using ``bufsize=0``, to fix ``run_cmd_qa`` missing output (`#3130 `_) + * update pip & install wheel package in generated Singularity container recipes (`#3136 `_) + * avoid crash in ``modify_env`` & unset ``unset_env_vars`` when using (older versions) of Python 3.5 & 3.6 by using ``list(...)`` (`#3140 `_) + * take into account that lib64 could be a symlink to lib (or vice versa) in ``get_software_libdir`` function (`#3141 `_) + * only parse docstring if it exists in ``gen_easyblock_doc_section_rst`` function (`#3144 `_) + * only add useful entries for ``$CPATH``, ``$(LD_)LIBRARY_PATH`` and ``$PATH`` (non-empty directories) (`#3145 `_, `#3152 `_) + * fix ``--list-software=detailed`` when using Python 3 by leveraging ``sort_looseversions`` function from ``py2vs3`` module (`#3146 `_) + * ensure subdirectories in software install directory have correct search (exec) permission (`#3147 `_) + * take into account that a checksum value may be a tuple of valid checksum in ``EasyBlock.check_checksums`` (`#3153 `_) + +* other changes: + + * bump to Lmod 8.2.9 in GitHub CI config (`#3115 `_) + * update copyright statements for 2020 (`#3149 `_) + * make Hound CI code style checker ignore "Black would make changes" produced by flake8-black (`#3162 `_) + +**easyblocks** + +* new software-specific easyblock for cryptography (to fix missing ``-pthread`` for all versions) (`#1874 `_) +* minor enhancements, including: + + * update WPS easyblock for v3.6 & newer (`#1315 `_) + * update FSL easyblock to support FSL v6.0.2 & newer (`#1860 `_) + * add ``setup_cmake_env`` function in CMakeMake easyblock which can be leveraged in other easyblocks, and use it for OpenFOAM (`#1869 `_) + * remove obsolete configure options for Python + build with optimizations/LTO enabled for recent Python versions (`#1876 `_) + * update WPS easyblock for recent versions: set ``$WRF_DIR`` to point to location of WRF installation (`#1886 `_) + * make sure ``$LIBLAPACK_MT`` is set before using it in ESMF easyblock (`#1887 `_) + * remove useless ``PATH`` entries + add ``PKG_CONFIG_PATH`` in imkl easyblock (`#1900 `_) + * enhance tbb easyblock to support building on POWER (`#1912 `_) + * enhance TensorFlow easyblock to pick up on ``--cuda-compute-capabilities``, and issue a warning if no CUDA compute capabilities are specified (`#1913 `_) + * add custom easyconfig parameter ``build_type`` to generic CMakeMake easyblock (`#1915 `_, `#1922 `_) + +* various bug fixes, including: + + * fix for conda packages that rely on particular versions of Python (`#1836 `_) + * fix path for intel and netCDF lib directories in NCL easyblock (`#1862 `_) + * fix CUDA 10.1 installation on POWER (`#1871 `_) + * change Bazel easyblock to prefer using Java dependency rather than included JDK (fix for POWER9) (`#1875 `_) + * remove optarch warning in GROMACS for Cray toolchains (`#1879 `_) + * also fix ``$WM_COMPILE_OPTION`` in OpenFOAM rc scripts to make debug builds work correctly (`#1880 `_) + * limit MPI ranks used for running WRF test cases to max. 4 + include contents of rsl.error.0000 output file in case test failed (`#1884 `_) + * update ``$PYTHONPATH`` + add ``python -c 'import mrtrix3'`` as sanity check command for recent MRtrix versions (`#1889 `_) + * update sanity check in SAMtools easyblock for version 1.10 (`#1890 `_) + * make sure ``$PYTHONNOUSERSITE`` it set when performing sanity check for (bundles of) Python package(s) (`#1891 `_) + * fix install dir subdir for WPS v4.0+ that is considered for ``$PATH`` and ``$LD_LIBRARY_PATH`` (`#1895 `_) + * impi: don't rebuild libfabric if the source code is not present (`#1896 `_) + * also copy component patches to self.cfg in Bundle generic easyblock (`#1897 `_) + * skip patch step in Bundle generic easyblock (per-component patches are still applied) (`#1898 `_) + * derive easyblock for iccifort only from icc easyblock (not ifort), to avoid adding include subdir to ``$CPATH`` (`#1899 `_) + * add ``export LANG=C`` to preinstallopts instead of install_script path in CUDA easyblock (`#1902 `_) + * stop setting updating ``$CPATH`` and ``$LIBRARY_PATH`` for GCC and GCCcore, not required (`#1903 `_) + * remove ``$LIBRARY_PATH`` entries in iccifort easyblock, already known to icc et al (`#1904 `_) + * use major/minor version of Python command being used if ``req_py_majver``/``req_py_minver`` are not specified (`#1907 `_) + * define ``$EB_PYTHON`` in module for EasyBuild installation, to make sure correct Python version is used at runtime (`#1908 `_) + * fix Python easyblock to allow configuring build of Python v3.8 (``Setup.dist`` script was renamed to ``Setup``) (`#1909 `_) + * fix netCDF easyblock for version 4.4.0 (`#1911 `_) + * correct comment about when we set ``RUNPARALLEL`` in HDF5 easyblock (`#1914 `_) + * do not sanity check on MATLAB compiler, since it requires a separate license (`#1916 `_) + * build HDF5 without MPI C++ extension to avoid breaking linkage for C software that requires HDF5 (`#1918 `_, `#1919 `_) + * override ``set_pylibdirs`` method in ``VersionIndependentPythonPackage`` to hard set ``self.pylibdir`` to 'lib' (`#1924 `_) + +* other changes: + + * increase timeout for interactive installation command in CUDA easyblock to 1000 sec. (`#1878 `_) + * disable running of ``sudo apt-get update`` in GitHub CI config, since it's failing (and we don't really need it) (`#1882 `_) + * stop requiring Python dep for SWIG, just configure with ``--without-python`` if Python is not a dependency (`#1894 `_) + * update copyright statements for 2020 (`#1905 `_) + * make Hound CI code style checker ignore "Black would make changes" produced by flake8-black (`#1923 `_) + +**easyconfigs** + +* added example easyconfig files for 27 new software packages: + + * Autoconf-archive (`#9658 `_), breseq (`#9603 `_), CrossMap (`#9483 `_), CSBDeep (`#9560 `_), CNT-ILP (`#9323 `_), cytoolz (`#9453 `_), Faber (`#9553 `_), + Fiji (`#8748 `_), GARLI (`#9404 `_), Globus-CLI (`#9565 `_), GtkSourceView (`#9526 `_), gradunwarp (`#9648 `_), gsettings-desktop-schemas (`#9529 `_), + HyPhy (`#9405 `_), horton (`#7449 `_), IGMPlot (`#9438 `_), LEMON (`#9323 `_), Meld (`#9530 `_), mhcflurry (`#9554 `_), NCIPLOT (`#9419 `_), ncl (`#9632 `_), + OpenSlide (`#9499 `_), openslide-python (`#9499 `_), pythran (`#9488 `_, `#9594 `_), Qualimap (`#9411 `_), TinyDB (`#9555 `_), TreeShrink (`#9381 `_) + +* added additional easyconfigs for various supported software packages, including: + + * Beast 1.10.4, Boost.Python 1.71.0, Clang 9.0.1, ESMF 8.0.0, FSL 6.0.3, fastp 0.20.0, freeglut 3.2.1, GDAL 3.0.2, + GEOS 3.8.0, GROMACS 2019.4, GSL 2.6, hwloc 2.1.0, Jellyfish 2.3.0, Julia 1.3.1, LibTIFF 4.1.0, libxml2 2.9.10, + lxml 4.4.2, Mothur 1.43.0, mayavi 4.7.1, molmod 1.4.5, netCDF-C++4 4.3.1, netCDF-Fortran 4.5.2, numactl 2.0.13, + OpenFOAM 7, OpenFOAM v1912, OpenMM 7.4.1, OpenMPI 4.0.2, PLUMED 2.5.3, PROJ 6.2.1, plotly.py 4.4.1, + pocl 1.4, QuickFF 2.2.4, R 3.6.2 w/ foss/2019b and fosscuda/2019b, ReFrame 2.20, SAMtools 1.10, SUNDIALS 5.1.0, + SWIG 4.0.1, Salmon 1.0.0, SuiteSparse 5.6.0, snakemake 5.7.1, TensorFlow 2.1.0 w/ fosscuda/2019b, torchvision 0.4.2, + WPS 4.1, WRF 4.1.3 + +* added easyconfigs for ``intel/2020.00`` toolchain (`#9575 `_) + +* minor enhancements, including: + + * add POWER9 support to CUDA 10.1 easyconfigs (`#9442 `_) + * build CMake in parallel (`#9543 `_) + * use NCCL for GPU ops in Horovod 0.18.2 easyconfig (`#9562 `_) + * update Java/1.8 wrapper to Java/1.8.0_231 (for x86_64) (`#9585 `_) + +* various bug fixes, including: + + * fix remote launch of broker and workers for SCOOP (`#9366 `_) + * fix failing RPATH sanity check for NCL 6.6.2 due to missing dependencies (+ add easyconfig using ``foss/2018b``) (`#9388 `_) + * add missing 'wheel' extensions to Spark 2.4.0 easyconfig using ``intel/2018b`` toolchain (`#9424 `_) + * add missing OS dependencies in Java 1.8 easyconfig used on POWER systems (`#9454 `_) + * fix build of recent Bazel versions on Power9 + stick to Java/1.8 as dependency (`#9455 `_) + * fix CMake 3.15.3 build on Power (+ enable building in parallel) (`#9469 `_) + * fix source URLs in xorg-macros easyconfigs (`#9477 `_, `#9578 `_) + * add missing wcwidth extension to Python 2.7.15 + 2.7.16 easyconfigs & enable 'pip check' in sanity check (`#9479 `_) + * remove (wrong) ``GI_TYPELIB_PATH`` and ``XDG_DATA_DIRS`` in various easyconfigs (`#9528 `_, `#9577 `_, `#9615 `_) + * use xorg-macros as dependency in X11 easyconfigs (rather than installing it as a bundle component) (`#9546 `_) + * fix lpsymphony extension for R-bundle-Bioconductor (`#9548 `_) + * add correct 'old-versions' source URL to all Mesa easyconfigs (`#9569 `_) + * add missing SHA256 checksums for Armadillo (`#9572 `_) + * also define ``$AUGUSTUS_BIN_PATH`` and ``$AUGUSTUS_SCRIPTS_PATH`` in generated module file for AUGUSTUS (`#9579 `_) + * add SSL OS dependencies for GDAL 3.0.0 (`#9586 `_) + * add missing jupyter_contrib_core extension for IPython 7.7.0+ + consistently include jupyter_nbextensions_configurator extension (`#9587 `_) + * patch libcxx (Clang 8.0.0) on pcc64le for incomplete IBM128 long double in GCC (`#9590 `_) + * patch for GCCcore 8.2.0 to fix '__float128 is not supported on this target' on ppc64le (`#9591 `_) + * fix broken easyconfigs for cyvcf2 v0.11.5 by adding missing 'monotonic' extension (`#9601 `_) + * use absolute path for extraction to allow relocating the build dir for g2log-1.0 (`#9604 `_) + * add alternate SHA256 checksum for kallisto-0.43.1 after re-release under same version without code changes (`#9611 `_) + * add additional valid checksum for MASS 7.3-51.4 extension in R 3.6.0 easyconfigs (`#9621 `_) + * update ctffind website (`#9622 `_) + * make sure we use easybuild Clang in pocl easyconfigs (`#9624 `_) + * make ``postinstallcmds`` independent of current working directory in OpenCV 3.1.0 easyconfigs (`#9628 `_) + * update ``source_urls`` to include old releases folder in libsodium easyconfigs (`#9632 `_) + * fix source URLs for ant v1.10.5 - v1.10.7 (`#9633 `_) + * update URLs to new location of libxc (`#9635 `_) + * add alternate SHA256 checksum for rda_1.0.2-2.1 extension in R 3.6.0 (`#9644 `_) + * update source URLs in QCA 2.1.0 easyconfigs (`#9647 `_) + * fix Python 3.5.1 easyconfig: bitstring 3.1.3 sources no longer available on PyPI (`#9649 `_) + * fix tesseract 4.1.0 dependencies (`#9650 `_) + * make ICU 64.2 depend on Python3 instead of Python 2, to avoid picking up system Python 3.x (`#9652 `_) + * use ``True`` (boolean value) rather than ``'True'`` (string value) for boolean easyconfig parameters (`#9657 `_) + * fix pyfits easyconfig by adding missing d2to1 extension (`#9687 `_) + +* other changes: + + * disable running of ``sudo apt-get update`` in GitHub CI config, since it's failing (and we don't really need it) (`#9492 `_) + * require that ``sanity_pip_check`` is enabled in new/changed easyconfigs (`#9516 `_, `#9576 `_) + * update copyright statements for 2020 (`#9598 `_) + * allow missing '-Python-*' versionsuffix for existing easyconfig files changed in PRs (`#9634 `_) + .. _release_notes_eb410: EasyBuild v4.1.0 (December 4th 2019) diff --git a/docs/conf.py b/docs/conf.py index 2298b5e3..ff66c81c 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 = '4.1.0' # this is meant to reference the version of EasyBuild +version = '4.1.1' # this is meant to reference the version of EasyBuild # The full version, including alpha/beta/rc tags. -release = '20191204.0' # this is meant to reference the version of the documentation itself +release = '20200116.0' # 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/scripts/gen_api_docs.py b/docs/scripts/gen_api_docs.py index c0d8001f..937ec6f5 100644 --- a/docs/scripts/gen_api_docs.py +++ b/docs/scripts/gen_api_docs.py @@ -28,10 +28,12 @@ @author Caroline De Brouwer (Ghent University) """ +from __future__ import print_function + import os import subprocess -from vsc.utils.generaloption import simple_option +from easybuild.base.generaloption import simple_option options = { @@ -49,5 +51,5 @@ # -f forces to overwrite existing files # -e specifies that every module is written in a separate file cmd = "sphinx-apidoc -o %s %s -f -e" % (so.options.out_folder, so.options.module) -print "$ %s" % cmd +print("$ %s" % cmd) subprocess.call(cmd, shell=True) diff --git a/docs/scripts/gen_easyblocks_docs.py b/docs/scripts/gen_easyblocks_docs.py index 7f08ad43..67df2ebc 100644 --- a/docs/scripts/gen_easyblocks_docs.py +++ b/docs/scripts/gen_easyblocks_docs.py @@ -28,10 +28,12 @@ @author Caroline De Brouwer (Ghent University) """ +from __future__ import print_function + import os import easybuild.tools.config as config -from vsc.utils.generaloption import simple_option +from easybuild.base.generaloption import simple_option from easybuild.tools.docs import gen_easyblocks_overview_rst from easybuild.tools.filetools import write_file @@ -66,7 +68,7 @@ txt = '\n'.join(autogen_comment + easyblocks_overview) if so.options.out_file: write_file(so.options.out_file, txt) - print '%s updated' % so.options.out_file + print('%s updated' % so.options.out_file) else: - print txt + print(txt) diff --git a/docs/version-specific/Supported_software.rst b/docs/version-specific/Supported_software.rst index 484654c0..af1167be 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 1770 different software packages (incl. toolchains, bundles): +EasyBuild |version| supports 1798 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_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_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` .. _list_software_ABAQUS_445: @@ -677,6 +677,7 @@ version toolchain ``2018.12`` ``system`` ``2019.03`` ``system`` ``2019.07`` ``system`` +``2019.10`` ``system`` =========== ========== @@ -701,6 +702,7 @@ version toolchain ``2018.12`` ``system`` ``2019.03`` ``system`` ``2019.07`` ``system`` +``2019.10`` ``system`` =========== ========== @@ -1060,7 +1062,7 @@ 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`` +``3.7.0`` ``foss/2019a``, ``foss/2019b`` ========= ================================================================================ @@ -1486,12 +1488,28 @@ Autoconf is an extensible package of M4 macros that produce shell scripts to au *homepage*: http://www.gnu.org/software/autoconf/ -======== =================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== -version toolchain -======== =================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== -``2.68`` ``foss/2016b`` -``2.69`` ``GCC/4.8.2``, ``GCC/4.8.4``, ``GCC/4.9.2``, ``GCC/4.9.3``, ``GCC/4.9.3-2.25``, ``GCC/5.2.0``, ``GCC/5.4.0-2.26``, ``GCCcore/4.9.2``, ``GCCcore/4.9.3``, ``GCCcore/5.3.0``, ``GCCcore/5.4.0``, ``GCCcore/6.1.0``, ``GCCcore/6.2.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``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`` -======== =================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== +======== ====================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== +version toolchain +======== ====================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== +``2.68`` ``foss/2016b`` +``2.69`` ``GCC/4.8.2``, ``GCC/4.8.4``, ``GCC/4.9.2``, ``GCC/4.9.3``, ``GCC/4.9.3-2.25``, ``GCC/5.2.0``, ``GCC/5.4.0-2.26``, ``GCCcore/4.9.2``, ``GCCcore/4.9.3``, ``GCCcore/5.3.0``, ``GCCcore/5.4.0``, ``GCCcore/6.1.0``, ``GCCcore/6.2.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.2.0``, ``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`` +======== ====================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== + + +.. _list_software_Autoconf-archive_1614: + +*Autoconf-archive* +++++++++++++++++++ + +The GNU Autoconf Archive is a collection of more than 500 macros for GNU Autoconf that have been contributed as free software by friendly supporters of the cause from all over the Internet. Every single one of those macros can be re-used without imposing any restrictions whatsoever on the licensing of the generated configure script. In particular, it is possible to use all those macros in configure scripts that are meant for non-free software. This policy is unusual for a Free Software Foundation project. The FSF firmly believes that software ought to be free, and software licenses like the GPL are specifically designed to ensure that derivative work based on free software must be free as well. In case of Autoconf, however, an exception has been made, because Autoconf is at such a pivotal position in the software development tool chain that the benefits from having this tool available as widely as possible outweigh the disadvantage that some authors may choose to use it, too, for proprietary software. + +*homepage*: https://www.gnu.org/software/autoconf-archive + +============== ==================== +version toolchain +============== ==================== +``2019.01.06`` ``GCC/8.2.0-2.31.1`` +============== ==================== .. _list_software_AutoDock_794: @@ -1549,7 +1567,7 @@ version toolchain Automake: GNU Standards-compliant Makefile generator -*homepage*: http://www.gnu.org/software/automake/automake.html +*homepage*: https://www.gnu.org/software/automake/automake.html ========== ===================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== version toolchain @@ -1559,7 +1577,7 @@ version toolchain ``1.14.1`` ``GCC/4.8.2`` ``1.15`` ``GCC/4.8.4``, ``GCC/4.9.2``, ``GCC/4.9.3``, ``GCC/4.9.3-2.25``, ``GCC/5.2.0``, ``GCC/5.4.0-2.26``, ``GCCcore/4.9.2``, ``GCCcore/4.9.3``, ``GCCcore/5.3.0``, ``GCCcore/5.4.0``, ``GCCcore/6.1.0``, ``GCCcore/6.2.0``, ``GCCcore/6.3.0``, ``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`` ``1.15.1`` ``GCCcore/6.4.0``, ``GCCcore/7.2.0`` -``1.16.1`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` +``1.16.1`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.2.0`` ========== ===================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== @@ -1578,7 +1596,7 @@ version toolchain ``20150119`` ``GCC/4.9.2`` ``20150215`` ``GCC/4.8.4``, ``GCC/4.9.2``, ``GCC/4.9.3``, ``GCC/4.9.3-2.25``, ``GCC/5.2.0``, ``GCC/5.4.0-2.26``, ``GCCcore/4.9.2``, ``GCCcore/4.9.3``, ``GCCcore/5.3.0``, ``GCCcore/5.4.0``, ``GCCcore/6.1.0``, ``GCCcore/6.2.0``, ``GCCcore/6.3.0``, ``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``, ``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`` ``20170619`` ``GCCcore/6.4.0``, ``GCCcore/7.2.0`` -``20180311`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` +``20180311`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.2.0`` ============ ====================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== @@ -1606,7 +1624,7 @@ 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_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_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` .. _list_software_Bader_478: @@ -1753,11 +1771,11 @@ Barrnap (BAsic Rapid Ribosomal RNA Predictor) predicts the location of ribosomal *homepage*: https://github.com/tseemann/barrnap -======= ============== -version toolchain -======= ============== -``0.9`` ``foss/2018b`` -======= ============== +======= ==================================== +version toolchain +======= ==================================== +``0.9`` ``GCC/8.2.0-2.31.1``, ``foss/2018b`` +======= ==================================== .. _list_software_basemap_729: @@ -2122,6 +2140,7 @@ version toolchain ========== ==================== ``1.8.4`` ``system`` ``1.10.1`` ``intel/2018a`` +``1.10.4`` ``GCC/8.2.0-2.31.1`` ``2.4.0`` ``foss/2016a`` ``2.4.7`` ``foss/2017a`` ``2.5.0`` ``foss/2018a`` @@ -2884,7 +2903,7 @@ version versionsuffix toolchain Boost.Python is a C++ library which enables seamless interoperability between C++ and the Python programming language. -*homepage*: http://boostorg.github.io/python +*homepage*: https://boostorg.github.io/python ========== ================== =================================================== version versionsuffix toolchain @@ -2896,6 +2915,7 @@ version versionsuffix toolchain ``1.67.0`` ``-Python-2.7.15`` ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b`` ``1.67.0`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` ``1.70.0`` ``gompi/2019a``, ``iimpi/2019a`` +``1.71.0`` ``gompi/2019b`` ========== ================== =================================================== @@ -3054,6 +3074,22 @@ version toolchain ========= =============== +.. _list_software_breseq_642: + +*breseq* +++++++++ + +breseq is a computational pipeline for the analysis of short-read re-sequencing data + +*homepage*: https://barricklab.org/breseq + +========== ============= =============== +version versionsuffix toolchain +========== ============= =============== +``0.35.0`` ``-R-3.6.0`` ``intel/2019a`` +========== ============= =============== + + .. _list_software_bsddb3_562: *bsddb3* @@ -3221,6 +3257,7 @@ version versionsuffix toolchain ``0.7.4`` ``-Python-2.7.13`` ``intel/2017a`` ``0.8.1`` ``-Python-2.7.14`` ``intel/2018a`` ``0.8.2`` ``-Python-3.6.6`` ``foss/2018b`` +``0.8.4`` ``foss/2019a`` ========= ================== =============== @@ -3281,7 +3318,7 @@ 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_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_CrossTalkZ_1008` - :ref:`list_software_CryptoMiniSat_1334` - :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_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_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` .. _list_software_C3D_186: @@ -3342,7 +3379,7 @@ version versionsuffix toolchain Cairo is a 2D graphics library with support for multiple output devices. Currently supported output targets include the X Window System (via both Xlib and XCB), Quartz, Win32, image buffers, PostScript, PDF, and SVG file output. Experimental backends include OpenGL, BeOS, OS/2, and DirectFB -*homepage*: http://cairographics.org +*homepage*: https://cairographics.org =========== ================ ================================================================ version versionsuffix toolchain @@ -3352,7 +3389,7 @@ version versionsuffix toolchain ``1.14.8`` ``intel/2017a`` ``1.14.10`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``intel/2017b`` ``1.14.12`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` -``1.16.0`` ``GCCcore/8.2.0`` +``1.16.0`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` =========== ================ ================================================================ @@ -3698,6 +3735,7 @@ version toolchain ``1.9.1`` ``intel/2017b`` ``1.9.2`` ``intel/2017b`` ``1.9.5`` ``intel/2018a``, ``intel/2018b``, ``iomkl/2018b`` +``1.9.8`` ``intel/2019b`` ========= ================================================= @@ -4161,7 +4199,7 @@ version versionsuffix toolchain C, C++, Objective-C compiler, based on LLVM. Does not include C++ standard library -- use libstdc++ from GCC. -*homepage*: http://clang.llvm.org/ +*homepage*: https://clang.llvm.org/ ========= ================== ====================================== version versionsuffix toolchain @@ -4183,6 +4221,8 @@ version versionsuffix toolchain ``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`` ========= ================== ====================================== @@ -4360,7 +4400,7 @@ version toolchain CMake, the cross-platform, open-source build system. CMake is a family of tools designed to build, test and package software. -*homepage*: http://www.cmake.org +*homepage*: https://www.cmake.org ========== ================================================================================================================================================= version toolchain @@ -4400,6 +4440,22 @@ version toolchain ========== ================================================================================================================================================= +.. _list_software_CNT-ILP_503: + +*CNT-ILP* ++++++++++ + +Integer Linear Program for the Copy-Number Tree Problem + +*homepage*: https://compbio.cs.brown.edu/projects/cnt-ilp/ + +============ ==================== +version toolchain +============ ==================== +``20171031`` ``GCC/8.2.0-2.31.1`` +============ ==================== + + .. _list_software_CNVkit_559: *CNVkit* @@ -4545,12 +4601,12 @@ Connectome Workbench is an open source, freely available visualization and disc *homepage*: https://www.humanconnectome.org/software/connectome-workbench -========= =============================== -version toolchain -========= =============================== -``1.2.2`` ``system`` -``1.3.2`` ``foss/2017b``, ``intel/2017b`` -========= =============================== +========= ================================================== +version toolchain +========= ================================================== +``1.2.2`` ``system`` +``1.3.2`` ``GCCcore/8.2.0``, ``foss/2017b``, ``intel/2017b`` +========= ================================================== .. _list_software_Control-FREEC_1139: @@ -4882,6 +4938,22 @@ version toolchain ======== ========================================================= +.. _list_software_CrossMap_808: + +*CrossMap* +++++++++++ + +CrossMap is a program for genome coordinates conversion between different assemblies (such as hg18 (NCBI36) <=> hg19 (GRCh37)). It supports commonly used file formats including BAM, CRAM, SAM, Wiggle, BigWig, BED, GFF, GTF and VCF. + +*homepage*: http://crossmap.sourceforge.net + +========= ================= ============== +version versionsuffix toolchain +========= ================= ============== +``0.3.9`` ``-Python-3.7.2`` ``foss/2019a`` +========= ================= ============== + + .. _list_software_CrossTalkZ_1008: *CrossTalkZ* @@ -4898,6 +4970,22 @@ version toolchain ======= ============== +.. _list_software_CRPropa_663: + +*CRPropa* ++++++++++ + +CRPropa is a publicly available code to study the propagation of ultra high energy nuclei up to iron on their voyage through an extra galactic environment. + +*homepage*: https://crpropa.desy.de + +========= ================= ============== +version versionsuffix toolchain +========= ================= ============== +``3.1.5`` ``-Python-3.7.2`` ``foss/2019a`` +========= ================= ============== + + .. _list_software_CryptoMiniSat_1334: *CryptoMiniSat* @@ -4914,6 +5002,22 @@ version versionsuffix toolchain ========= ================== =============== +.. _list_software_CSBDeep_598: + +*CSBDeep* ++++++++++ + +CSBDeep is a toolbox for Content-aware Image Restoration (CARE). + +*homepage*: https://csbdeep.bioimagecomputing.com/ + +========= ================= ================================== +version versionsuffix toolchain +========= ================= ================================== +``0.4.1`` ``-Python-3.7.2`` ``foss/2019a``, ``fosscuda/2019a`` +========= ================= ================================== + + .. _list_software_cscope_637: *cscope* @@ -4969,7 +5073,7 @@ version toolchain Program for finding CTFs of electron micrographs. -*homepage*: http://grigoriefflab.janelia.org/ctffind4 +*homepage*: https://grigoriefflab.umassmed.edu/ctffind4 ========== ================================== version toolchain @@ -5099,6 +5203,7 @@ version versionsuffix toolchain ``7.4.2.24`` ``-CUDA-10.0.130`` ``system`` ``7.6.2.24`` ``-CUDA-10.1.243`` ``system`` ``7.6.4.38`` ``gcccuda/2019a``, ``gcccuda/2019b`` +``7.6.4.38`` ``-CUDA-10.0.130`` ``system`` ============ ================== =========================================================== @@ -5298,6 +5403,22 @@ version versionsuffix toolchain =========== ================== =============================== +.. _list_software_cytoolz_788: + +*cytoolz* ++++++++++ + +Cython implementation of the toolz package, which provides high performance utility functions for iterables, functions, and dictionaries. + +*homepage*: https://github.com/pytoolz/cytoolz + +========== ================= ================= +version versionsuffix toolchain +========== ================= ================= +``0.10.1`` ``-Python-3.7.2`` ``GCCcore/8.2.0`` +========== ================= ================= + + .. _list_software_cytosim_776: *cytosim* @@ -5647,6 +5768,7 @@ DCMTK is a collection of libraries and applications implementing large parts the version toolchain ========= ================= ``3.6.3`` ``GCCcore/7.3.0`` +``3.6.5`` ``GCCcore/8.2.0`` ========= ================= @@ -5762,6 +5884,7 @@ version versionsuffix toolchain ========= ================= =============== ``2.5.4`` ``-Python-3.6.3`` ``intel/2017b`` ``3.3.1`` ``-Python-3.6.6`` ``foss/2018b`` +``3.3.1`` ``-Python-3.7.4`` ``intel/2019b`` ========= ================= =============== @@ -6339,6 +6462,7 @@ version toolchain ``3.9.4`` ``system`` ``4.0.0`` ``system`` ``4.0.1`` ``system`` +``4.1.0`` ``system`` ========== ========== @@ -6374,6 +6498,7 @@ version toolchain ``2.8.2`` ``intel/2018a`` ``2.9.2`` ``intel/2018b``, ``iomkl/2018b`` ``2.12.5`` ``gompi/2019a`` +``2.15.0`` ``iimpi/2019b`` ========== ================================ @@ -6590,12 +6715,12 @@ EMBOSS is 'The European Molecular Biology Open Software Suite'. EMBOSS is a fre *homepage*: http://emboss.sourceforge.net/ -========= ================= ========================================================================================================== -version versionsuffix toolchain -========= ================= ========================================================================================================== -``6.6.0`` ``foss/2016b``, ``foss/2018b``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``intel/2017a``, ``intel/2018b`` -``6.6.0`` ``-X11-20170314`` ``intel/2017a`` -========= ================= ========================================================================================================== +========= ================= ================================================================================================================================ +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`` ``-X11-20170314`` ``intel/2017a`` +========= ================= ================================================================================================================================ .. _list_software_emcee_511: @@ -6722,7 +6847,7 @@ version versionsuffix toolchain The Earth System Modeling Framework (ESMF) is software for building and coupling weather, climate, and related models. -*homepage*: http://sourceforge.net/projects/esmf +*homepage*: https://sourceforge.net/projects/esmf ============ ================ ================================================================= version versionsuffix toolchain @@ -6732,6 +6857,7 @@ version versionsuffix toolchain ``7.0.0`` ``foss/2016a`` ``7.0.2`` ``intel/2017b`` ``7.1.0r`` ``foss/2018b``, ``intel/2018a``, ``intel/2018b``, ``iomkl/2018b`` +``8.0.0`` ``intel/2019b`` ============ ================ ================================================================= @@ -6942,7 +7068,7 @@ version toolchain --- -:ref:`list_software_f90cache_707` - :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_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-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` .. _list_software_f90cache_707: @@ -6961,6 +7087,22 @@ version toolchain ======== ========== +.. _list_software_Faber_480: + +*Faber* ++++++++ + +Faber started as a clone of Boost.Build, to experiment with a new Python frontend. Meanwhile it has evolved into a new build system, which retains most of the features found in Boost.Build, but with (hopefully !) much simplified logic, in addition of course to using Python as scripting language, rather than Jam. The original bjam engine is still in use as scheduler, though at this point that is mostly an implementation detail. + +*homepage*: https://stefanseefeld.github.io/faber + +======= ================= +version toolchain +======= ================= +``0.3`` ``GCCcore/8.3.0`` +======= ================= + + .. _list_software_faceswap_842: *faceswap* @@ -7096,15 +7238,16 @@ version toolchain *fastp* +++++++ -A tool designed to provide fast all-in-one preprocessing for FastQ files. This tool is developed in C++ with multithreading supported to afford high performance. +A tool designed to provide fast all-in-one preprocessing for FastQ files. This tool is developed in C++ with multithreading supported to afford high performance. *homepage*: https://github.com/OpenGene/fastp -========== ============== -version toolchain -========== ============== -``0.19.7`` ``foss/2018b`` -========== ============== +========== ============================================= +version toolchain +========== ============================================= +``0.19.7`` ``foss/2018b`` +``0.20.0`` ``GCC/8.2.0-2.31.1``, ``iccifort/2019.5.281`` +========== ============================================= .. _list_software_fastPHASE_799: @@ -7508,17 +7651,17 @@ FFTW is a C subroutine library for computing the discrete Fourier transform (DFT *homepage*: http://www.fftw.org -========= ============= ======================================================================================================================================================================================== -version versionsuffix toolchain -========= ============= ======================================================================================================================================================================================== -``2.1.5`` ``intel/2016b``, ``intel/2017a``, ``intel/2018b`` -``3.3.4`` ``gmpich/2016a``, ``gmvapich2/1.7.20``, ``gmvapich2/2016a``, ``gompi/2016.04``, ``gompi/2016.06``, ``gompi/2016.07``, ``gompi/2016a``, ``gompi/2016b``, ``intel/2016a``, ``intel/2016b`` -``3.3.5`` ``gompi/2016.07``, ``gompi/2016.09``, ``gompi/2016b``, ``intel/2016b`` -``3.3.6`` ``gimpi/2017b``, ``gimpic/2017b``, ``gompi/2017a``, ``gompi/2017b``, ``gompic/2017b``, ``intel/2016b``, ``intel/2017a``, ``intel/2017b``, ``intelcuda/2017b`` -``3.3.7`` ``gimkl/2017a``, ``gimpi/2018a``, ``gmpich/2017.08``, ``gompi/2018a``, ``gompic/2018a``, ``intel/2017b``, ``intel/2018.00``, ``intel/2018.01``, ``intel/2018a``, ``iomkl/2018a`` -``3.3.7`` ``-serial`` ``GCC/6.4.0-2.28`` -``3.3.8`` ``gompi/2018.08``, ``gompi/2018b``, ``gompi/2019a``, ``gompi/2019b``, ``gompic/2018b``, ``gompic/2019a``, ``gompic/2019b``, ``intel/2018b``, ``intel/2019a``, ``iomkl/2018b`` -========= ============= ======================================================================================================================================================================================== +========= ============= ============================================================================================================================================================================================== +version versionsuffix toolchain +========= ============= ============================================================================================================================================================================================== +``2.1.5`` ``intel/2016b``, ``intel/2017a``, ``intel/2018b`` +``3.3.4`` ``gmpich/2016a``, ``gmvapich2/1.7.20``, ``gmvapich2/2016a``, ``gompi/2016.04``, ``gompi/2016.06``, ``gompi/2016.07``, ``gompi/2016a``, ``gompi/2016b``, ``intel/2016a``, ``intel/2016b`` +``3.3.5`` ``gompi/2016.07``, ``gompi/2016.09``, ``gompi/2016b``, ``intel/2016b`` +``3.3.6`` ``gimpi/2017b``, ``gimpic/2017b``, ``gompi/2017a``, ``gompi/2017b``, ``gompic/2017b``, ``intel/2016b``, ``intel/2017a``, ``intel/2017b``, ``intelcuda/2017b`` +``3.3.7`` ``gimkl/2017a``, ``gimpi/2018a``, ``gmpich/2017.08``, ``gompi/2018a``, ``gompic/2018a``, ``intel/2017b``, ``intel/2018.00``, ``intel/2018.01``, ``intel/2018a``, ``iomkl/2018a`` +``3.3.7`` ``-serial`` ``GCC/6.4.0-2.28`` +``3.3.8`` ``gompi/2018.08``, ``gompi/2018b``, ``gompi/2019a``, ``gompi/2019b``, ``gompic/2018b``, ``gompic/2019a``, ``gompic/2019b``, ``intel/2018b``, ``intel/2019a``, ``intel/2019b``, ``iomkl/2018b`` +========= ============= ============================================================================================================================================================================================== .. _list_software_FGSL_300: @@ -7554,6 +7697,23 @@ version versionsuffix toolchain ============ ================== =============================== +.. _list_software_Fiji_386: + +*Fiji* +++++++ + +Fiji is an image processing package—a 'batteries-included' distribution of ImageJ, bundling a lot of plugins which facilitate scientific image analysis. This release is based on ImageJ 2.0.0-rc-69/1.52p. + +*homepage*: https://fiji.sc/ + +================= ========== +version toolchain +================= ========== +``20170530`` ``system`` +``20191119-2057`` ``system`` +================= ========== + + .. _list_software_file_416: *file* @@ -7846,14 +8006,14 @@ version toolchain FLTK is a cross-platform C++ GUI toolkit for UNIX/Linux (X11), Microsoft Windows, and MacOS X. FLTK provides modern GUI functionality without the bloat and supports 3D graphics via OpenGL and its built-in GLUT emulation. -*homepage*: http://www.fltk.org +*homepage*: https://www.fltk.org ========= =================================================================================================================================================================================================== version toolchain ========= =================================================================================================================================================================================================== ``1.3.3`` ``foss/2016a``, ``foss/2016b``, ``intel/2016a``, ``intel/2016b`` ``1.3.4`` ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``fosscuda/2017b``, ``fosscuda/2018a``, ``fosscuda/2018b``, ``intel/2017a``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b``, ``intelcuda/2017b`` -``1.3.5`` ``GCC/8.2.0-2.31.1`` +``1.3.5`` ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0`` ========= =================================================================================================================================================================================================== @@ -8180,6 +8340,7 @@ version versionsuffix toolchain ========= ================ ====================================================================================================================================================================================== ``3.0.0`` ``GCCcore/8.2.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a``, ``intel/2017b``, ``intel/2018a`` ``3.0.0`` ``-Mesa-11.2.1`` ``foss/2016a``, ``intel/2016a`` +``3.2.1`` ``GCCcore/8.3.0`` ========= ================ ====================================================================================================================================================================================== @@ -8287,20 +8448,23 @@ version toolchain FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data. -*homepage*: http://www.fmrib.ox.ac.uk/fsl/ - -========== ================== ================================================ -version versionsuffix toolchain -========== ================== ================================================ -``5.0.9`` ``intel/2016a`` -``5.0.9`` ``-Mesa-11.2.1`` ``intel/2016a`` -``5.0.9`` ``-centos6_64`` ``system`` -``5.0.10`` ``foss/2017b``, ``intel/2017a``, ``intel/2017b`` -``5.0.11`` ``foss/2018b`` -``5.0.11`` ``-Python-3.6.6`` ``foss/2018b`` -``6.0.1`` ``-Python-2.7.15`` ``foss/2019a`` -``6.0.1`` ``-Python-3.7.2`` ``foss/2019a`` -========== ================== ================================================ +*homepage*: https://www.fmrib.ox.ac.uk/fsl/ + +========== ============================== ================================================ +version versionsuffix toolchain +========== ============================== ================================================ +``5.0.9`` ``intel/2016a`` +``5.0.9`` ``-Mesa-11.2.1`` ``intel/2016a`` +``5.0.9`` ``-centos6_64`` ``system`` +``5.0.10`` ``foss/2017b``, ``intel/2017a``, ``intel/2017b`` +``5.0.11`` ``foss/2018b`` +``5.0.11`` ``-Python-3.6.6`` ``foss/2018b`` +``6.0.1`` ``-Python-2.7.15`` ``foss/2019a`` +``6.0.1`` ``-Python-3.7.2`` ``foss/2019a`` +``6.0.2`` ``-Python-2.7.15`` ``foss/2018b`` +``6.0.2`` ``-Python-2.7.15-CUDA-9.2.88`` ``foss/2018b`` +``6.0.3`` ``-Python-3.7.4`` ``foss/2019b`` +========== ============================== ================================================ .. _list_software_FSLeyes_667: @@ -8426,7 +8590,7 @@ 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_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_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_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_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_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_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` .. _list_software_g2clib_563: @@ -8438,11 +8602,11 @@ Library contains GRIB2 encoder/decoder ('C' version). *homepage*: http://www.nco.ncep.noaa.gov/pmb/codes/GRIB2/ -========= ================================================================== -version toolchain -========= ================================================================== -``1.6.0`` ``intel/2017a``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b`` -========= ================================================================== +========= ===================================================================================================== +version toolchain +========= ===================================================================================================== +``1.6.0`` ``GCCcore/8.3.0``, ``foss/2018b``, ``intel/2017a``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b`` +========= ===================================================================================================== .. _list_software_g2lib_464: @@ -8454,12 +8618,12 @@ Library contains GRIB2 encoder/decoder and search/indexing routines. *homepage*: http://www.nco.ncep.noaa.gov/pmb/codes/GRIB2/ -========= ================================================= -version toolchain -========= ================================================= -``1.4.0`` ``intel/2017a``, ``intel/2017b``, ``intel/2018a`` -``3.1.0`` ``intel/2018b`` -========= ================================================= +========= ================================================== +version toolchain +========= ================================================== +``1.4.0`` ``intel/2017a``, ``intel/2017b``, ``intel/2018a`` +``3.1.0`` ``GCCcore/8.3.0``, ``foss/2018b``, ``intel/2018b`` +========= ================================================== .. _list_software_g2log_475: @@ -8562,6 +8726,22 @@ version toolchain ========= =============== +.. _list_software_GARLI_367: + +*GARLI* ++++++++ + +GARLI, Genetic Algorithm for Rapid Likelihood Inference is a program for inferring phylogenetic trees. Using an approach similar to a classical genetic algorithm, it rapidly searches the space of evolutionary trees and model parameters to find the solution maximizing the likelihood score. It implements nucleotide, amino acid and codon-based models of sequence evolution, and runs on all platforms. + +*homepage*: https://code.google.com/archive/p/garli/ + +======== =============== +version toolchain +======== =============== +``2.01`` ``gompi/2019a`` +======== =============== + + .. _list_software_GAT_220: *GAT* @@ -8692,6 +8872,7 @@ version toolchain ``7.6.0`` ``GCCcore/6.4.0`` ``7.6.4`` ``GCCcore/7.3.0`` ``7.6.10`` ``GCCcore/8.2.0`` +``7.6.12`` ``GCCcore/8.3.0`` ========== ================================== @@ -8915,8 +9096,9 @@ version versionsuffix toolchain ``2.2.3`` ``-Python-3.6.3`` ``foss/2017b`` ``2.2.3`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a``, ``iomkl/2018a`` ``2.2.3`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` -``3.0.0`` ``-Python-2.7.15`` ``foss/2019a`` +``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`` ========= ============================== ================================================================ @@ -9273,7 +9455,7 @@ version versionsuffix toolchain *GEOS* ++++++ -GEOS (Geometry Engine - Open Source) is a C++ port of the Java Topology Suite (JTS) +GEOS (Geometry Engine - Open Source) is a C++ port of the Java Topology Suite (JTS) *homepage*: https://trac.osgeo.org/geos @@ -9291,8 +9473,9 @@ version versionsuffix toolchain ``3.6.2`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b``, ``intel/2018.01`` ``3.6.2`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a``, ``iomkl/2018a`` ``3.6.2`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` -``3.7.2`` ``-Python-2.7.15`` ``foss/2019a`` +``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`` ========= ================== ================================================================ @@ -9347,7 +9530,7 @@ version versionsuffix toolchain ``0.19.8`` ``GCCcore/4.9.3``, ``GCCcore/5.4.0``, ``foss/2016.04``, ``foss/2016b``, ``intel/2016b``, ``system`` ``0.19.8.1`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``system`` ``0.19.8.1`` ``-libxml2-2.9.7`` ``GCCcore/6.4.0`` -``0.20.1`` ``GCCcore/8.3.0`` +``0.20.1`` ``GCCcore/8.3.0``, ``system`` ============ ================== =================================================================================================== @@ -9382,6 +9565,7 @@ version toolchain ========== ================= ``0.9.12`` ``foss/2016b`` ``0.10.6`` ``GCCcore/7.3.0`` +``0.11.6`` ``GCCcore/8.3.0`` ========== ================= @@ -9442,7 +9626,7 @@ version toolchain Ghostscript is a versatile processor for PostScript data with the ability to render PostScript to different targets. It used to be part of the cups printing stack, but is no longer used for that. -*homepage*: http://ghostscript.com +*homepage*: https://ghostscript.com ======== ================== ================================================== version versionsuffix toolchain @@ -9455,6 +9639,7 @@ version versionsuffix toolchain ``9.23`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` ``9.23`` ``-cairo-1.14.12`` ``GCCcore/6.4.0`` ``9.27`` ``GCCcore/8.2.0`` +``9.50`` ``GCCcore/8.3.0`` ======== ================== ================================================== @@ -9669,6 +9854,7 @@ GitPython is a python library used to interact with Git repositories version versionsuffix toolchain ========== ================= =============================== ``2.1.11`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` +``3.0.3`` ``-Python-3.7.2`` ``GCCcore/8.2.0`` ========== ================= =============================== @@ -9797,6 +9983,7 @@ version toolchain ======== ================= ``2.17`` ``GCCcore/6.4.0`` ``2.26`` ``GCCcore/6.4.0`` +``2.30`` ``GCCcore/8.3.0`` ======== ================= @@ -9807,13 +9994,13 @@ version toolchain C++ bindings for Glib -*homepage*: http://www.gtk.org/ +*homepage*: https://www.gtk.org/ -========== ================= -version toolchain -========== ================= -``2.49.7`` ``GCCcore/8.2.0`` -========== ================= +========== ======================================================= +version toolchain +========== ======================================================= +``2.49.7`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` +========== ======================================================= .. _list_software_GLIMMER_525: @@ -9883,6 +10070,22 @@ version versionsuffix toolchain ======= ============= =============== +.. _list_software_Globus-CLI_881: + +*Globus-CLI* +++++++++++++ + +A Command Line Wrapper over the Globus SDK for Python, which provides an interface to Globus services from the shell, and is suited to both interactive and simple scripting use cases. + +*homepage*: https://docs.globus.org/cli/ + +========== ================= +version toolchain +========== ================= +``1.11.0`` ``GCCcore/8.3.0`` +========== ================= + + .. _list_software_GlobusConnectPersonal_2170: *GlobusConnectPersonal* @@ -10490,6 +10693,22 @@ version toolchain ========= ========== +.. _list_software_gradunwarp_1083: + +*gradunwarp* +++++++++++++ + +Gradient Unwarping. This is the Human Connectome Project fork of the no longer maintained original. + +*homepage*: https://github.com/Washington-University/gradunwarp + +========= ====================== ============== +version versionsuffix toolchain +========= ====================== ============== +``1.1.0`` ``-HCP-Python-2.7.15`` ``foss/2019a`` +========= ====================== ============== + + .. _list_software_graph-tool_1021: *graph-tool* @@ -10514,7 +10733,7 @@ version versionsuffix toolchain Graphene is a a thin layer of types for graphic libraries -*homepage*: http://ebassi.github.io/graphene/ +*homepage*: https://ebassi.github.io/graphene/ ========= =============== version toolchain @@ -10726,7 +10945,8 @@ version versionsuffix toolchain ``2018.4`` ``-PLUMED-2.5.0`` ``foss/2018b``, ``fosscuda/2018b`` ``2019`` ``foss/2018b``, ``fosscuda/2018b`` ``2019.2`` ``fosscuda/2019a`` -``2019.3`` ``foss/2019a``, ``fosscuda/2019a`` +``2019.3`` ``foss/2019a``, ``foss/2019b``, ``fosscuda/2019a``, ``fosscuda/2019b`` +``2019.4`` ``foss/2019b`` ========== ================= ============================================================================================================ @@ -10762,6 +10982,22 @@ version versionsuffix toolchain ========= ================== ============== +.. _list_software_gsettings-desktop-schemas_2576: + +*gsettings-desktop-schemas* ++++++++++++++++++++++++++++ + +gsettings-desktop-schemas contains a collection of GSettings schemas for settings shared by various components of a desktop. + +*homepage*: https://gitlab.gnome.org/GNOME/gsettings-desktop-schemas + +========== ================= +version toolchain +========== ================= +``3.34.0`` ``GCCcore/8.2.0`` +========== ================= + + .. _list_software_GSL_230: *GSL* @@ -10769,7 +11005,7 @@ version versionsuffix toolchain The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. The library provides a wide range of mathematical routines such as random number generators, special functions and least-squares fitting. -*homepage*: http://www.gnu.org/software/gsl/ +*homepage*: https://www.gnu.org/software/gsl/ ========= ============================================================================================================================ version toolchain @@ -10780,6 +11016,7 @@ version toolchain ``2.3`` ``foss/2016b``, ``foss/2017a``, ``intel/2016b``, ``intel/2017a`` ``2.4`` ``GCCcore/6.4.0`` ``2.5`` ``GCC/7.3.0-2.30``, ``GCC/8.2.0-2.31.1``, ``iccifort/2018.3.222-GCC-7.3.0-2.30``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1`` +``2.6`` ``GCC/8.3.0``, ``iccifort/2019.5.281`` ========= ============================================================================================================================ @@ -10806,7 +11043,7 @@ version toolchain GStreamer is a library for constructing graphs of media-handling components. The applications it supports range from simple Ogg/Vorbis playback, audio/video streaming to complex audio (mixing) and video (non-linear editing) processing. -*homepage*: http://gstreamer.freedesktop.org/ +*homepage*: https://gstreamer.freedesktop.org/ =========== ================================================================================================================== version toolchain @@ -10825,7 +11062,7 @@ version toolchain GStreamer is a library for constructing graphs of media-handling components. The applications it supports range from simple Ogg/Vorbis playback, audio/video streaming to complex audio (mixing) and video (non-linear editing) processing. -*homepage*: http://gstreamer.freedesktop.org/ +*homepage*: https://gstreamer.freedesktop.org/ =========== ================================================================================================================== version toolchain @@ -10893,6 +11130,23 @@ version toolchain =========== ================================================================================ +.. _list_software_GtkSourceView_1330: + +*GtkSourceView* ++++++++++++++++ + +GtkSourceView is a GNOME library that extends GtkTextView, the standard GTK+ widget for multiline text editing. GtkSourceView adds support for syntax highlighting, undo/redo, file loading and saving, search and replace, a completion system, printing, displaying line numbers, and other features typical of a source code editor. + +*homepage*: https://wiki.gnome.org/Projects/GtkSourceView + +=========== ================= +version toolchain +=========== ================= +``3.24.11`` ``GCCcore/8.2.0`` +``4.4.0`` ``GCCcore/8.2.0`` +=========== ================= + + .. _list_software_GTOOL_389: *GTOOL* @@ -10918,12 +11172,12 @@ GTS stands for the GNU Triangulated Surface Library. It is an Open Source Free *homepage*: http://gts.sourceforge.net/ -============ ================================================================================================= -version toolchain -============ ================================================================================================= -``0.7.6`` ``foss/2016a``, ``foss/2016b``, ``foss/2018b``, ``intel/2016a``, ``intel/2016b``, ``intel/2018a`` -``20121130`` ``foss/2017b`` -============ ================================================================================================= +============ ================================================================================================================= +version toolchain +============ ================================================================================================================= +``0.7.6`` ``foss/2016a``, ``foss/2016b``, ``foss/2018b``, ``foss/2019b``, ``intel/2016a``, ``intel/2016b``, ``intel/2018a`` +``20121130`` ``foss/2017b`` +============ ================================================================================================================= .. _list_software_guenomu_768: @@ -10951,14 +11205,14 @@ Guile is a programming language, designed to help programmers create flexible a *homepage*: https://www.gnu.org/software/guile/ -========== ================================================================================================================================================================================ -version toolchain -========== ================================================================================================================================================================================ -``1.8.8`` ``GCCcore/5.4.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GNU/4.9.3-2.25``, ``foss/2016a``, ``foss/2016b``, ``foss/2017a``, ``intel/2016a``, ``intel/2016b`` -``2.0.11`` ``GCC/4.9.3-2.25``, ``foss/2016a`` -``2.2.2`` ``GCCcore/6.4.0`` -``2.2.4`` ``GCCcore/7.3.0`` -========== ================================================================================================================================================================================ +========== =================================================================================================================================================================================================== +version toolchain +========== =================================================================================================================================================================================================== +``1.8.8`` ``GCCcore/5.4.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GNU/4.9.3-2.25``, ``foss/2016a``, ``foss/2016b``, ``foss/2017a``, ``intel/2016a``, ``intel/2016b`` +``2.0.11`` ``GCC/4.9.3-2.25``, ``foss/2016a`` +``2.2.2`` ``GCCcore/6.4.0`` +``2.2.4`` ``GCCcore/7.3.0`` +========== =================================================================================================================================================================================================== .. _list_software_GULP_312: @@ -10982,20 +11236,22 @@ version toolchain *Gurobi* ++++++++ -The Gurobi Optimizer is a state-of-the-art solver for mathematical programming. The solvers in the Gurobi Optimizer were designed from the ground up to exploit modern architectures and multi-core processors, using the most advanced implementations of the latest algorithms. +The Gurobi Optimizer is a state-of-the-art solver for mathematical programming. The solvers in the Gurobi Optimizer were designed from the ground up to exploit modern architectures and multi-core processors, using the most advanced implementations of the latest algorithms. -*homepage*: http://www.gurobi.com +*homepage*: https://www.gurobi.com -========= ================= =============== -version versionsuffix toolchain -========= ================= =============== -``6.5.1`` ``system`` -``6.5.2`` ``system`` -``7.0.1`` ``system`` -``7.5.2`` ``system`` -``7.5.2`` ``-Python-3.6.4`` ``intel/2018a`` -``8.1.1`` ``system`` -========= ================= =============== +========= ================= =============================== +version versionsuffix toolchain +========= ================= =============================== +``6.5.1`` ``system`` +``6.5.2`` ``system`` +``7.0.1`` ``system`` +``7.5.2`` ``system`` +``7.5.2`` ``-Python-3.6.4`` ``intel/2018a`` +``8.1.1`` ``system`` +``9.0.0`` ``system`` +``9.0.0`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` +========= ================= =============================== .. _list_software_gzip_442: @@ -11022,7 +11278,7 @@ version toolchain --- -:ref:`list_software_h4toh5_540` - :ref:`list_software_H5hut_462` - :ref:`list_software_h5py_390` - :ref:`list_software_Hadoop_603` - :ref:`list_software_hanythingondemand_1808` - :ref:`list_software_HAPGEN2_485` - :ref:`list_software_HarfBuzz_812` - :ref:`list_software_Harminv_725` - :ref:`list_software_HBase_451` - :ref:`list_software_HDDM_285` - :ref:`list_software_HDF_210` - :ref:`list_software_HDF5_263` - :ref:`list_software_hdf5storage_1116` - :ref:`list_software_HDFView_621` - :ref:`list_software_HEALPix_587` - :ref:`list_software_heaptrack_947` - :ref:`list_software_Hello_500` - :ref:`list_software_help2man_791` - :ref:`list_software_HH-suite_743` - :ref:`list_software_HiC-Pro_594` - :ref:`list_software_HiCExplorer_1093` - :ref:`list_software_HIPS_308` - :ref:`list_software_HISAT2_427` - :ref:`list_software_HLAminer_752` - :ref:`list_software_HMMER_377` - :ref:`list_software_hmmlearn_852` - :ref:`list_software_HOME_297` - :ref:`list_software_Horovod_737` - :ref:`list_software_HPCG_290` - :ref:`list_software_HPCX_307` - :ref:`list_software_HPDBSCAN_579` - :ref:`list_software_HPL_228` - :ref:`list_software_htop_443` - :ref:`list_software_HTSeq_453` - :ref:`list_software_HTSlib_550` - :ref:`list_software_hub_319` - :ref:`list_software_hunspell_875` - :ref:`list_software_hwloc_541` - :ref:`list_software_Hyperopt_859` - :ref:`list_software_hyperspy_900` - :ref:`list_software_hypothesis_1104` - :ref:`list_software_Hypre_520` +:ref:`list_software_h4toh5_540` - :ref:`list_software_H5hut_462` - :ref:`list_software_h5py_390` - :ref:`list_software_Hadoop_603` - :ref:`list_software_hanythingondemand_1808` - :ref:`list_software_HAPGEN2_485` - :ref:`list_software_HarfBuzz_812` - :ref:`list_software_Harminv_725` - :ref:`list_software_HBase_451` - :ref:`list_software_HDDM_285` - :ref:`list_software_HDF_210` - :ref:`list_software_HDF5_263` - :ref:`list_software_hdf5storage_1116` - :ref:`list_software_HDFView_621` - :ref:`list_software_HEALPix_587` - :ref:`list_software_heaptrack_947` - :ref:`list_software_Hello_500` - :ref:`list_software_help2man_791` - :ref:`list_software_HH-suite_743` - :ref:`list_software_HiC-Pro_594` - :ref:`list_software_HiCExplorer_1093` - :ref:`list_software_HIPS_308` - :ref:`list_software_HISAT2_427` - :ref:`list_software_HLAminer_752` - :ref:`list_software_HMMER_377` - :ref:`list_software_hmmlearn_852` - :ref:`list_software_HOME_297` - :ref:`list_software_Horovod_737` - :ref:`list_software_horton_666` - :ref:`list_software_HPCG_290` - :ref:`list_software_HPCX_307` - :ref:`list_software_HPDBSCAN_579` - :ref:`list_software_HPL_228` - :ref:`list_software_htop_443` - :ref:`list_software_HTSeq_453` - :ref:`list_software_HTSlib_550` - :ref:`list_software_hub_319` - :ref:`list_software_hunspell_875` - :ref:`list_software_hwloc_541` - :ref:`list_software_Hyperopt_859` - :ref:`list_software_hyperspy_900` - :ref:`list_software_HyPhy_498` - :ref:`list_software_hypothesis_1104` - :ref:`list_software_Hypre_520` .. _list_software_h4toh5_540: @@ -11180,7 +11436,7 @@ version toolchain HarfBuzz is an OpenType text shaping engine. -*homepage*: http://www.freedesktop.org/wiki/Software/HarfBuzz +*homepage*: https://www.freedesktop.org/wiki/Software/HarfBuzz ========= ================================================ version toolchain @@ -11252,17 +11508,17 @@ version versionsuffix toolchain HDF (also known as HDF4) is a library and multi-object file format for storing and managing data between machines. -*homepage*: http://www.hdfgroup.org/products/hdf4/ +*homepage*: https://www.hdfgroup.org/products/hdf4/ -========== ============== ======================================================= -version versionsuffix toolchain -========== ============== ======================================================= -``4.2.11`` ``intel/2016a`` -``4.2.12`` ``intel/2017a`` -``4.2.13`` ``GCCcore/6.4.0`` -``4.2.13`` ``-no-netcdf`` ``intel/2017a`` -``4.2.14`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` -========== ============== ======================================================= +========== ============== ========================================================================== +version versionsuffix toolchain +========== ============== ========================================================================== +``4.2.11`` ``intel/2016a`` +``4.2.12`` ``intel/2017a`` +``4.2.13`` ``GCCcore/6.4.0`` +``4.2.13`` ``-no-netcdf`` ``intel/2017a`` +``4.2.14`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` +========== ============== ========================================================================== .. _list_software_HDF5_263: @@ -11292,7 +11548,7 @@ version versionsuffix toolchain ``1.10.0-patch1`` ``foss/2016b``, ``intel/2016b``, ``intel/2017.01``, ``intel/2017a`` ``1.10.1`` ``foss/2017a``, ``foss/2017b``, ``foss/2018a``, ``fosscuda/2017b``, ``intel/2017a``, ``intel/2017b``, ``intel/2018.00``, ``intel/2018.01``, ``intel/2018a``, ``intelcuda/2017b``, ``iomkl/2017b``, ``iomkl/2018a`` ``1.10.2`` ``PGI/18.4-GCC-6.4.0-2.28``, ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b``, ``iomkl/2018b`` -``1.10.5`` ``gompi/2019a``, ``gompi/2019b``, ``gompic/2019a``, ``gompic/2019b``, ``iimpi/2019a``, ``iimpi/2019b``, ``iimpic/2019a`` +``1.10.5`` ``gompi/2019a``, ``gompi/2019b``, ``gompic/2019a``, ``gompic/2019b``, ``iimpi/2019a``, ``iimpi/2019b``, ``iimpic/2019a``, ``iimpic/2019b`` ================= ============= ================================================================================================================================================================================================================== @@ -11556,13 +11812,30 @@ Horovod is a distributed training framework for TensorFlow. *homepage*: https://github.com/uber/horovod -========== ================================== ================== -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-2.0.0-Python-3.7.4`` ``fosscuda/2019b`` -========== ================================== ================== +========== =================================== ================== +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-2.0.0-Python-3.7.4`` ``fosscuda/2019b`` +========== =================================== ================== + + +.. _list_software_horton_666: + +*horton* +++++++++ + +HORTON is a Helpful Open-source Research TOol for N-fermion systems, written primarily in the Python programming language. (HORTON is named after the helpful pachyderm, not the Canadian caffeine supply store.) The ultimate goal of HORTON is to provide a platform for testing new ideas on the quantum many-body problem at a reasonable computational cost. Although HORTON is primarily designed to be a quantum-chemistry program, it can perform computations involving model Hamiltonians, and could be extended for computations in nuclear physics. + +*homepage*: https://theochem.github.io/horton + +========= ================== =============================== +version versionsuffix toolchain +========= ================== =============================== +``2.1.1`` ``-Python-2.7.15`` ``foss/2018b``, ``intel/2018b`` +========= ================== =============================== .. _list_software_HPCG_290: @@ -11628,7 +11901,7 @@ version toolchain ======= ========================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================= ``2.1`` ``foss/2016.04``, ``foss/2016.06``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``gmpolf/2016a``, ``gmvolf/1.7.20``, ``gmvolf/2016a``, ``intel/2016.00``, ``intel/2016.01``, ``intel/2016.02-GCC-4.9``, ``intel/2016.02-GCC-5.3``, ``intel/2016.03-GCC-4.9``, ``intel/2016.03-GCC-5.3``, ``intel/2016.03-GCC-5.4``, ``intel/2016a``, ``intel/2016b``, ``iomkl/2016.07``, ``pomkl/2016.03``, ``pomkl/2016.04``, ``pomkl/2016.09`` ``2.2`` ``foss/2016.07``, ``foss/2016.09``, ``foss/2017a``, ``foss/2017b``, ``foss/2018.08``, ``foss/2018a``, ``foss/2018b``, ``fosscuda/2017b``, ``fosscuda/2018a``, ``fosscuda/2018b``, ``gimkl/2018b``, ``giolf/2017b``, ``giolf/2018a``, ``giolfc/2017b``, ``gmpolf/2017.10``, ``gomkl/2018b``, ``intel/2017.00``, ``intel/2017.01``, ``intel/2017.02``, ``intel/2017.09``, ``intel/2017a``, ``intel/2017b``, ``intel/2018.00``, ``intel/2018.01``, ``intel/2018.02``, ``intel/2018.04``, ``intel/2018a``, ``intel/2018b``, ``intel/2019.00``, ``intel/2019.01``, ``intelcuda/2016.10``, ``intelcuda/2017b``, ``iomkl/2016.09-GCC-4.9.3-2.25``, ``iomkl/2016.09-GCC-5.4.0-2.26``, ``iomkl/2017.01``, ``iomkl/2017a``, ``iomkl/2017b``, ``iomkl/2018.02``, ``iomkl/2018a``, ``iomkl/2018b``, ``pomkl/2016.09`` -``2.3`` ``CrayCCE/19.06``, ``CrayGNU/19.06``, ``CrayIntel/19.06``, ``foss/2019a``, ``foss/2019b``, ``fosscuda/2019b``, ``gomkl/2019a``, ``intel/2019.02``, ``intel/2019.03``, ``intel/2019a``, ``intel/2019b``, ``intelcuda/2019b``, ``iomkl/2019.01`` +``2.3`` ``CrayCCE/19.06``, ``CrayGNU/19.06``, ``CrayIntel/19.06``, ``foss/2019a``, ``foss/2019b``, ``fosscuda/2019b``, ``gomkl/2019a``, ``intel/2019.02``, ``intel/2019.03``, ``intel/2019a``, ``intel/2019b``, ``intel/2020.00``, ``intelcuda/2019b``, ``iomkl/2019.01`` ======= ========================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================= @@ -11764,6 +12037,7 @@ version toolchain ``1.11.12`` ``GCCcore/8.3.0`` ``2.0.2`` ``GCCcore/8.2.0`` ``2.0.3`` ``GCCcore/8.3.0`` +``2.1.0`` ``GCCcore/9.2.0`` =========== ===================================================================================================================================================================================================================================================== @@ -11800,6 +12074,22 @@ version versionsuffix toolchain ========= ================= =============== +.. _list_software_HyPhy_498: + +*HyPhy* ++++++++ + +HyPhy (Hypothesis Testing using Phylogenies) is an open-source software package for the analysis of genetic sequences (in particular the inference of natural selection) using techniques in phylogenetics, molecular evolution, and machine learning + +*homepage*: https://veg.github.io/hyphy-site/ + +========= =============== +version toolchain +========= =============== +``2.5.1`` ``gompi/2019a`` +========= =============== + + .. _list_software_hypothesis_1104: *hypothesis* @@ -11842,7 +12132,7 @@ 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_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_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` .. _list_software_i-cisTarget_1084: @@ -11989,6 +12279,7 @@ version versionsuffix toolchain ``2019.3.199`` ``-GCC-8.3.0-2.32`` ``system`` ``2019.4.243`` ``system`` ``2019.5.281`` ``system`` +``2020.0.166`` ``system`` ``system`` ``-GCC-system-2.29`` ``system`` ============== ===================== ========== @@ -12051,13 +12342,14 @@ version versionsuffix toolchain ICU is a mature, widely used set of C/C++ and Java libraries providing Unicode and Globalization support for software applications. -*homepage*: http://site.icu-project.org/home +*homepage*: https://site.icu-project.org/home ======== ==================================== version toolchain ======== ==================================== ``61.1`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` -``64.2`` ``GCCcore/8.2.0`` +``64.2`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` +``65.1`` ``GCCcore/8.3.0`` ======== ==================================== @@ -12134,6 +12426,22 @@ version versionsuffix toolchain ============== ===================== ========== +.. _list_software_IGMPlot_636: + +*IGMPlot* ++++++++++ + +IGMPlot is a free open-source program developed to identify molecular interactions and prepare data to build 2D and 3D representations of them in the molecular environment. + +*homepage*: http://igmplot.univ-reims.fr + +========= ====================================== +version toolchain +========= ====================================== +``2.4.2`` ``GCC/8.3.0``, ``iccifort/2019.5.281`` +========= ====================================== + + .. _list_software_igraph_635: *igraph* @@ -12226,6 +12534,7 @@ version versionsuffix toolchain ``2019.03`` ``system`` ``2019a`` ``system`` ``2019b`` ``system`` +``2020.00`` ``system`` ``system`` ``-GCC-system-2.29`` ``system`` =========== ==================== ========== @@ -12324,7 +12633,7 @@ version toolchain ImageMagick is a software suite to create, edit, compose, or convert bitmap images -*homepage*: http://www.imagemagick.org/ +*homepage*: https://www.imagemagick.org/ ============ =================================== =============================== version versionsuffix toolchain @@ -12345,6 +12654,7 @@ version versionsuffix toolchain ``7.0.7-39`` ``-Ghostscript-9.23-cairo-1.14.12`` ``GCCcore/6.4.0`` ``7.0.8-11`` ``GCCcore/7.3.0`` ``7.0.8-46`` ``GCCcore/8.2.0`` +``7.0.9-5`` ``GCCcore/8.3.0`` ============ =================================== =============================== @@ -12424,7 +12734,7 @@ version versionsuffix toolchain Intel Math Kernel Library is a library of highly optimized, extensively threaded math routines for science, engineering, and financial applications that require maximum performance. Core math functions include BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more. -*homepage*: https://software.intel.com/en-us/intel-mkl/ +*homepage*: https://software.intel.com/mkl ============== ====================================================================================================================================================================================================================================================================== version toolchain @@ -12449,6 +12759,7 @@ version toolchain ``2019.2.187`` ``iimpi/2019.02`` ``2019.3.199`` ``iimpi/2019.03`` ``2019.5.281`` ``iimpi/2019b``, ``iimpic/2019b`` +``2020.0.166`` ``iimpi/2020.00`` ============== ====================================================================================================================================================================================================================================================================== @@ -12525,6 +12836,7 @@ 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`` ``system`` ``iccifort/system-GCC-system-2.29`` ============== ============= ================================================================================================================================================================================================================================ @@ -12725,6 +13037,7 @@ version versionsuffix toolchain ``2019.03`` ``system`` ``2019a`` ``system`` ``2019b`` ``system`` +``2020.00`` ``system`` =========== ============= ========== @@ -12944,7 +13257,7 @@ version toolchain Intel Integrated Performance Primitives (Intel IPP) is an extensive library of multicore-ready, highly optimized software functions for multimedia, data processing, and communications applications. Intel IPP offers thousands of optimized functions covering frequently used fundamental algorithms. -*homepage*: http://software.intel.com/en-us/articles/intel-ipp/ +*homepage*: https://software.intel.com/en-us/articles/intel-ipp/ ============== ========== version toolchain @@ -13129,7 +13442,7 @@ version toolchain The Intel Trace Collector is a low-overhead tracing library that performs event-based tracing in applications. The Intel Trace Analyzer provides a convenient way to monitor application activities gathered by the Intel Trace Collector through graphical displays. -*homepage*: http://software.intel.com/en-us/intel-trace-analyzer/ +*homepage*: https://software.intel.com/en-us/intel-trace-analyzer/ ============== ========== version toolchain @@ -13177,12 +13490,13 @@ ITS Tool allows you to translate your XML documents with PO files *homepage*: http://itstool.org/ -========= ================== =============== -version versionsuffix toolchain -========= ================== =============== -``2.0.5`` ``-Python-2.7.14`` ``intel/2018a`` -``2.0.5`` ``-Python-2.7.15`` ``foss/2018b`` -========= ================== =============== +========= ================== ================= +version versionsuffix toolchain +========= ================== ================= +``2.0.5`` ``-Python-2.7.14`` ``intel/2018a`` +``2.0.5`` ``-Python-2.7.15`` ``foss/2018b`` +``2.0.6`` ``-Python-3.7.2`` ``GCCcore/8.2.0`` +========= ================== ================= .. _list_software_letter_j: @@ -13295,6 +13609,7 @@ version toolchain ``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`` @@ -13350,6 +13665,7 @@ version toolchain ``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`` ========== =============================== @@ -13372,6 +13688,7 @@ version toolchain ``5.0.1`` ``GCCcore/6.4.0`` ``5.1.0`` ``GCCcore/7.3.0`` ``5.2.0`` ``GCCcore/8.2.0`` +``5.2.1`` ``GCCcore/8.3.0`` ========= =============================== @@ -13504,6 +13821,7 @@ version versionsuffix toolchain ========= ================= ========== ``1.1.1`` ``-linux-x86_64`` ``system`` ``1.2.0`` ``-linux-x86_64`` ``system`` +``1.3.1`` ``-linux-x86_64`` ``system`` ========= ================= ========== @@ -13748,11 +14066,12 @@ KMC is a disk-based programm for counting k-mers from (possibly gzipped) FASTQ/F *homepage*: http://sun.aei.polsl.pl/kmc -========= ============================== -version toolchain -========= ============================== -``3.1.0`` ``foss/2018a``, ``foss/2018b`` -========= ============================== +========= ================= ============================== +version versionsuffix toolchain +========= ================= ============================== +``3.1.0`` ``foss/2018a``, ``foss/2018b`` +``3.1.1`` ``-Python-3.7.2`` ``GCC/8.2.0-2.31.1`` +========= ================= ============================== .. _list_software_KmerGenie_887: @@ -13944,7 +14263,7 @@ 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_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_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` .. _list_software_L_RNA_scaffolder_1540: @@ -14061,6 +14380,22 @@ version toolchain ========= ========== +.. _list_software_LEMON_379: + +*LEMON* ++++++++ + +LEMON stands for Library for Efficient Modeling and Optimization in Networks. It is a C++ template library providing efficient implementations of common data structures and algorithms with focus on combinatorial optimization tasks connected mainly with graphs and networks. + +*homepage*: https://lemon.cs.elte.hu + +========= ==================== +version toolchain +========= ==================== +``1.3.1`` ``GCC/8.2.0-2.31.1`` +========= ==================== + + .. _list_software_Leptonica_927: *Leptonica* @@ -14193,6 +14528,7 @@ version toolchain ``1.5`` ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``foss/2016b``, ``intel/2016b``, ``intel/2017a`` ``1.7`` ``GCCcore/7.3.0`` ``1.11`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` +``1.13`` ``GCCcore/8.3.0`` ======== ========================================================================================================= @@ -14513,14 +14849,14 @@ GD is an open source code library for the dynamic creation of images by programm *homepage*: https://libgd.github.io/ -========= ========================================================================================= -version toolchain -========= ========================================================================================= -``2.1.1`` ``foss/2016a``, ``intel/2016a`` -``2.2.3`` ``foss/2016b``, ``intel/2016b`` -``2.2.4`` ``GCCcore/6.4.0``, ``foss/2016b``, ``intel/2017a`` -``2.2.5`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``intel/2017b``, ``intel/2018a`` -========= ========================================================================================= +========= ============================================================================================================ +version toolchain +========= ============================================================================================================ +``2.1.1`` ``foss/2016a``, ``intel/2016a`` +``2.2.3`` ``foss/2016b``, ``intel/2016b`` +``2.2.4`` ``GCCcore/6.4.0``, ``foss/2016b``, ``intel/2017a`` +``2.2.5`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``intel/2017b``, ``intel/2018a`` +========= ============================================================================================================ .. _list_software_libgeotiff_1051: @@ -14536,7 +14872,7 @@ Library for reading and writing coordinate system information from/to GeoTIFF fi version toolchain ========= =============================================== ``1.4.2`` ``foss/2018a``, ``foss/2018b``, ``intel/2018b`` -``1.5.1`` ``GCCcore/8.2.0`` +``1.5.1`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` ========= =============================================== @@ -14721,6 +15057,7 @@ Libiconv converts from one character encoding to another through Unicode convers version toolchain ======== ======================================================= ``1.15`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` +``1.16`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` ======== ======================================================= @@ -14756,7 +15093,7 @@ version toolchain ========= ================================================================================================================================================================== ``1.1.4`` ``intel/2016a`` ``1.1.6`` ``GCC/8.2.0-2.31.1``, ``foss/2016b``, ``foss/2018a``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``intel/2016b``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b`` -``2.0.3`` ``gompi/2019a`` +``2.0.3`` ``foss/2018b``, ``gompi/2019a``, ``intel/2018b`` ``2.1.0`` ``intel/2016b`` ``2.4.2`` ``intel/2018a`` ``2.5.0`` ``gompi/2019a``, ``iimpi/2019a`` @@ -14796,11 +15133,11 @@ GNU libmatheval is a library (callable from C and Fortran) to parse and evaluat *homepage*: http://www.gnu.org/software/libmatheval/ -========== ========================================================================================================================= -version toolchain -========== ========================================================================================================================= -``1.1.11`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``foss/2016b``, ``foss/2017a``, ``intel/2016a``, ``intel/2016b`` -========== ========================================================================================================================= +========== ============================================================================================================================================ +version toolchain +========== ============================================================================================================================================ +``1.1.11`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``foss/2016b``, ``foss/2017a``, ``intel/2016a``, ``intel/2016b`` +========== ============================================================================================================================================ .. _list_software_libmaus2_799: @@ -14842,13 +15179,14 @@ version toolchain Generic PCI access library. -*homepage*: http://cgit.freedesktop.org/xorg/lib/libpciaccess/ +*homepage*: https://cgit.freedesktop.org/xorg/lib/libpciaccess/ ========== ============================================================================================= version toolchain ========== ============================================================================================= ``0.13.4`` ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``intel/2016a``, ``intel/2016b`` ``0.14`` ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` +``0.16`` ``GCCcore/9.2.0`` ========== ============================================================================================= @@ -15039,13 +15377,13 @@ The libsigc++ package implements a typesafe callback system for standard C++. *homepage*: https://libsigcplusplus.github.io/libsigcplusplus/ -========== ================= -version toolchain -========== ================= -``2.10.0`` ``GCCcore/6.4.0`` -``2.10.1`` ``GCCcore/7.3.0`` -``2.10.2`` ``GCCcore/8.2.0`` -========== ================= +========== ==================================== +version toolchain +========== ==================================== +``2.10.0`` ``GCCcore/6.4.0`` +``2.10.1`` ``GCCcore/7.3.0`` +``2.10.2`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` +========== ==================================== .. _list_software_libsigsegv_1071: @@ -15087,14 +15425,14 @@ version toolchain Libsndfile is a C library for reading and writing files containing sampled sound (such as MS Windows WAV and the Apple/SGI AIFF format) through one standard library interface. -*homepage*: http://www.mega-nerd.com/libsndfile - -========== ======================================================================== -version toolchain -========== ======================================================================== -``1.0.28`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``intel/2017a`` -========== ======================================================================== - +*homepage*: http://www.mega-nerd.com/libsndfile + +========== =========================================================================================== +version toolchain +========== =========================================================================================== +``1.0.28`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``intel/2017a`` +========== =========================================================================================== + .. _list_software_libsodium_968: @@ -15103,7 +15441,7 @@ version toolchain Sodium is a modern, easy-to-use software library for encryption, decryption, signatures, password hashing and more. -*homepage*: http://doc.libsodium.org/ +*homepage*: https://doc.libsodium.org/ ========== ==================================== version toolchain @@ -15242,7 +15580,7 @@ version toolchain tiff: Library and tools for reading and writing TIFF data files -*homepage*: https://www.remotesensing.org/libtiff/ +*homepage*: https://libtiff.maptools.org/ ========== ========================================================================================================= version toolchain @@ -15252,6 +15590,7 @@ version toolchain ``4.0.8`` ``intel/2017a``, ``intel/2017b`` ``4.0.9`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``foss/2017b``, ``intel/2017b``, ``intel/2018.01``, ``intel/2018b`` ``4.0.10`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` +``4.1.0`` ``GCCcore/8.3.0`` ========== ========================================================================================================= @@ -15280,13 +15619,13 @@ GNU libtool is a generic library support script. Libtool hides the complexity of *homepage*: http://www.gnu.org/software/libtool -========= ==================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== -version toolchain -========= ==================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== -``2.4.2`` ``GCC/4.8.2``, ``GCC/4.9.2`` -``2.4.5`` ``GCC/4.8.4``, ``GCC/4.9.2`` -``2.4.6`` ``GCC/4.8.4``, ``GCC/4.9.2``, ``GCC/4.9.3``, ``GCC/4.9.3-2.25``, ``GCC/5.2.0``, ``GCC/5.4.0-2.26``, ``GCCcore/4.9.2``, ``GCCcore/4.9.3``, ``GCCcore/5.3.0``, ``GCCcore/5.4.0``, ``GCCcore/6.1.0``, ``GCCcore/6.2.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``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`` -========= ==================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== +========= ======================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================= +version toolchain +========= ======================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================= +``2.4.2`` ``GCC/4.8.2``, ``GCC/4.9.2`` +``2.4.5`` ``GCC/4.8.4``, ``GCC/4.9.2`` +``2.4.6`` ``GCC/4.8.4``, ``GCC/4.9.2``, ``GCC/4.9.3``, ``GCC/4.9.3-2.25``, ``GCC/5.2.0``, ``GCC/5.4.0-2.26``, ``GCCcore/4.9.2``, ``GCCcore/4.9.3``, ``GCCcore/5.3.0``, ``GCCcore/5.4.0``, ``GCCcore/6.1.0``, ``GCCcore/6.2.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.2.0``, ``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`` +========= ======================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================= .. _list_software_libunistring_1306: @@ -15304,7 +15643,7 @@ version toolchain ``0.9.3`` ``GCC/4.9.3-2.25``, ``GNU/4.9.3-2.25``, ``foss/2016a``, ``intel/2016a`` ``0.9.6`` ``GCCcore/5.4.0``, ``foss/2016b``, ``foss/2017a``, ``intel/2016b`` ``0.9.7`` ``GCCcore/6.4.0`` -``0.9.10`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` +``0.9.10`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` ========== ======================================================================= @@ -15431,12 +15770,12 @@ version toolchain Libxc is a library of exchange-correlation functionals for density-functional theory. The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals. -*homepage*: http://www.tddft.org/programs/octopus/wiki/index.php/Libxc +*homepage*: https://www.tddft.org/programs/libxc ========= ======================================================================================================================================= version toolchain ========= ======================================================================================================================================= -``2.2.2`` ``GCC/8.2.0-2.31.1`` +``2.2.2`` ``GCC/8.2.0-2.31.1``, ``foss/2018b``, ``intel/2018b`` ``2.2.3`` ``foss/2016b``, ``intel/2016a``, ``intel/2016b``, ``intel/2017b``, ``intel/2018a`` ``3.0.0`` ``GCC/5.4.0-2.26``, ``iccifort/2016.3.210-GCC-5.4.0-2.26``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a``, ``intel/2017b`` ``3.0.1`` ``GCC/8.2.0-2.31.1``, ``foss/2016b``, ``foss/2017a``, ``foss/2018a``, ``foss/2018b``, ``gimkl/2017a``, ``intel/2018a``, ``intel/2018b`` @@ -15636,11 +15975,11 @@ libxml++ is a C++ wrapper for the libxml XML parser library. *homepage*: http://libxmlplusplus.sourceforge.net -========== ================= -version toolchain -========== ================= -``2.40.1`` ``GCCcore/8.2.0`` -========== ================= +========== ======================================================= +version toolchain +========== ======================================================= +``2.40.1`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` +========== ======================================================= .. _list_software_libxml2_698: @@ -15652,21 +15991,22 @@ Libxml2 is the XML C parser and toolchain developed for the Gnome project (but *homepage*: http://xmlsoft.org/ -========= ================== ================================================================================================================================================================================== -version versionsuffix toolchain -========= ================== ================================================================================================================================================================================== -``2.9.2`` ``GCC/4.8.3``, ``GCC/4.8.4``, ``GCC/4.9.2``, ``GCC/4.9.3-2.25``, ``GNU/4.9.3-2.25`` -``2.9.3`` ``GCC/4.9.3-2.25``, ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a`` -``2.9.3`` ``-Python-2.7.11`` ``foss/2016a``, ``intel/2016a`` -``2.9.4`` ``GCC/5.4.0-2.26``, ``GCCcore/4.9.3``, ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``foss/2016.04``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2017a``, ``intel/2016b`` -``2.9.4`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` -``2.9.4`` ``-Python-2.7.13`` ``intel/2017a`` -``2.9.5`` ``GCCcore/6.3.0`` -``2.9.6`` ``GCCcore/6.4.0`` -``2.9.7`` ``GCCcore/6.4.0`` -``2.9.8`` ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` -``2.9.9`` ``GCCcore/8.3.0`` -========= ================== ================================================================================================================================================================================== +========== ================== ================================================================================================================================================================================== +version versionsuffix toolchain +========== ================== ================================================================================================================================================================================== +``2.9.2`` ``GCC/4.8.3``, ``GCC/4.8.4``, ``GCC/4.9.2``, ``GCC/4.9.3-2.25``, ``GNU/4.9.3-2.25`` +``2.9.3`` ``GCC/4.9.3-2.25``, ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a`` +``2.9.3`` ``-Python-2.7.11`` ``foss/2016a``, ``intel/2016a`` +``2.9.4`` ``GCC/5.4.0-2.26``, ``GCCcore/4.9.3``, ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``foss/2016.04``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2017a``, ``intel/2016b`` +``2.9.4`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` +``2.9.4`` ``-Python-2.7.13`` ``intel/2017a`` +``2.9.5`` ``GCCcore/6.3.0`` +``2.9.6`` ``GCCcore/6.4.0`` +``2.9.7`` ``GCCcore/6.4.0`` +``2.9.8`` ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` +``2.9.9`` ``GCCcore/8.3.0`` +``2.9.10`` ``GCCcore/9.2.0`` +========== ================== ================================================================================================================================================================================== .. _list_software_libxml2-python_1417: @@ -15678,12 +16018,13 @@ Libxml2 is the XML C parser and toolchain developed for the Gnome project (but *homepage*: http://xmlsoft.org/ -========= ================== =============== -version versionsuffix toolchain -========= ================== =============== -``2.9.7`` ``-Python-2.7.14`` ``intel/2018a`` -``2.9.8`` ``-Python-2.7.15`` ``foss/2018b`` -========= ================== =============== +========= ================== ================= +version versionsuffix toolchain +========= ================== ================= +``2.9.7`` ``-Python-2.7.14`` ``intel/2018a`` +``2.9.8`` ``-Python-2.7.15`` ``foss/2018b`` +``2.9.8`` ``-Python-3.7.2`` ``GCCcore/8.2.0`` +========= ================== ================= .. _list_software_libXmu_625: @@ -15784,6 +16125,7 @@ version versionsuffix toolchain ``1.1.30`` ``GCCcore/6.3.0`` ``1.1.32`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` ``1.1.33`` ``GCCcore/8.2.0`` +``1.1.34`` ``GCCcore/8.3.0`` ========== ================== ================================================================= @@ -15952,13 +16294,13 @@ Little CMS intends to be an OPEN SOURCE small-footprint color management engine, *homepage*: http://www.littlecms.com/ -======= ======================================================================================================== -version toolchain -======= ======================================================================================================== -``2.7`` ``intel/2016a`` -``2.8`` ``GCCcore/6.4.0``, ``foss/2016b``, ``intel/2016b``, ``intel/2017a`` -``2.9`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``foss/2017b``, ``foss/2018a``, ``intel/2017b`` -======= ======================================================================================================== +======= =========================================================================================================================== +version toolchain +======= =========================================================================================================================== +``2.7`` ``intel/2016a`` +``2.8`` ``GCCcore/6.4.0``, ``foss/2016b``, ``intel/2016b``, ``intel/2017a`` +``2.9`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``foss/2017b``, ``foss/2018a``, ``intel/2017b`` +======= =========================================================================================================================== .. _list_software_LLVM_315: @@ -16161,11 +16503,11 @@ Mixed Integer Linear Programming (MILP) solver *homepage*: https://sourceforge.net/projects/lpsolve/ -=========== ====================================================================================================================================================== -version toolchain -=========== ====================================================================================================================================================== -``5.5.2.5`` ``GCC/6.4.0-2.28``, ``foss/2018a``, ``iccifort/2017.4.196-GCC-6.4.0-2.28``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``intel/2017a``, ``intel/2018b`` -=========== ====================================================================================================================================================== +=========== ===================================================================================================================================================================== +version toolchain +=========== ===================================================================================================================================================================== +``5.5.2.5`` ``GCC/6.4.0-2.28``, ``GCC/8.3.0``, ``foss/2018a``, ``iccifort/2017.4.196-GCC-6.4.0-2.28``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``intel/2017a``, ``intel/2018b`` +=========== ===================================================================================================================================================================== .. _list_software_lrslib_648: @@ -16325,7 +16667,7 @@ version toolchain The lxml XML toolkit is a Pythonic binding for the C libraries libxml2 and libxslt. -*homepage*: http://lxml.de/ +*homepage*: https://lxml.de/ ========= ================== =============================== version versionsuffix toolchain @@ -16340,6 +16682,7 @@ version versionsuffix toolchain ``4.2.5`` ``-Python-2.7.15`` ``foss/2018b``, ``intel/2018b`` ``4.2.5`` ``-Python-3.6.6`` ``foss/2018b`` ``4.3.3`` ``GCCcore/8.2.0`` +``4.4.2`` ``GCCcore/8.3.0`` ========= ================== =============================== @@ -16401,7 +16744,7 @@ 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_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_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_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` .. _list_software_M4_129: @@ -16453,6 +16796,7 @@ version versionsuffix toolchain ``2.1.1.20160309`` ``-Python-2.7.14`` ``intel/2017b`` ``2.1.2.1`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` ``2.1.2.1`` ``-Python-2.7.15`` ``intel/2019a`` +``2.2.5`` ``-Python-3.6.6`` ``foss/2018b`` ================== ================== =============================== @@ -16598,15 +16942,15 @@ version versionsuffix toolchain GNU version of make utility -*homepage*: http://www.gnu.org/software/make/make.html +*homepage*: https://www.gnu.org/software/make/make.html -========= ================== -version toolchain -========= ================== -``3.82`` ``GCC/4.8.2`` -``4.1`` ``GCC/4.9.2`` -``4.2.1`` ``GCC/7.3.0-2.30`` -========= ================== +========= ===================================== +version toolchain +========= ===================================== +``3.82`` ``GCC/4.8.2`` +``4.1`` ``GCC/4.9.2`` +``4.2.1`` ``GCC/7.3.0-2.30``, ``GCCcore/8.3.0`` +========= ===================================== .. _list_software_makedepend_1038: @@ -16616,13 +16960,13 @@ version toolchain The makedepend package contains a C-preprocessor like utility to determine build-time dependencies. -*homepage*: http://www.linuxfromscratch.org/blfs/view/svn/x/makedepend.html +*homepage*: https://linux.die.net/man/1/makedepend ========= ======================================================================================= version toolchain ========= ======================================================================================= ``1.0.5`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a`` -``1.0.6`` ``GCCcore/7.3.0`` +``1.0.6`` ``GCCcore/7.3.0``, ``GCCcore/8.3.0`` ========= ======================================================================================= @@ -17036,6 +17380,7 @@ The Mayavi scientific data 3-dimensional visualizer version versionsuffix toolchain ========= ================== =============== ``4.4.4`` ``-Python-2.7.11`` ``intel/2016a`` +``4.7.1`` ``-Python-3.7.2`` ``foss/2019a`` ========= ================== =============== @@ -17163,6 +17508,7 @@ version versionsuffix toolchain ========= ================= =============== ``1.9.1`` ``-Python-3.6.3`` ``intel/2017b`` ``1.9.2`` ``-Python-3.6.6`` ``intel/2018b`` +``1.9.3`` ``-Python-3.7.4`` ``intel/2019b`` ========= ================= =============== @@ -17251,6 +17597,22 @@ version versionsuffix toolchain ========= ================== ============================== +.. _list_software_Meld_386: + +*Meld* +++++++ + +Meld is a visual diff and merge tool targeted at developers. Meld helps you compare files, directories, and version controlled projects. It provides two- and three-way comparison of both files and directories, and has support for many popular version control systems. + +*homepage*: https://meldmerge.org/ + +========== ================= ================= +version versionsuffix toolchain +========== ================= ================= +``3.20.1`` ``-Python-3.7.2`` ``GCCcore/8.2.0`` +========== ================= ================= + + .. _list_software_MEME_292: *MEME* @@ -17422,11 +17784,11 @@ Mesh-Quality Improvement Library *homepage*: https://software.sandia.gov/mesquite/ -========= ===================================================================== -version toolchain -========= ===================================================================== -``2.3.0`` ``GCCcore/6.4.0``, ``gimkl/2.11.5``, ``intel/2016a``, ``intel/2017a`` -========= ===================================================================== +========= ======================================================================================== +version toolchain +========= ======================================================================================== +``2.3.0`` ``GCCcore/6.4.0``, ``GCCcore/8.3.0``, ``gimkl/2.11.5``, ``intel/2016a``, ``intel/2017a`` +========= ======================================================================================== .. _list_software_MetaBAT_606: @@ -17594,6 +17956,22 @@ version versionsuffix toolchain ========= ============= =============================================================================================================================================================================================================== +.. _list_software_mhcflurry_988: + +*mhcflurry* ++++++++++++ + +MHCflurry implements class I peptide/MHC binding affinity prediction. By default it supports 112 MHC alleles using ensembles of allele-specific models. Pan-allele predictors supporting virtually any MHC allele of known sequence are available for testing (see below). MHCflurry runs on Python 2.7 and 3.4+ using the keras neural network library. It exposes command-line and Python library interfaces. + +*homepage*: https://github.com/openvax/mhcflurry + +========= ================= ================================== +version versionsuffix toolchain +========= ================= ================================== +``1.2.4`` ``-Python-3.7.2`` ``foss/2019a``, ``fosscuda/2019a`` +========= ================= ================================== + + .. _list_software_MiGEC_389: *MiGEC* @@ -17981,7 +18359,7 @@ version versionsuffix toolchain MolMod is a Python library with many compoments that are useful to write molecular modeling programs. -*homepage*: http://molmod.github.io/molmod/ +*homepage*: https://molmod.github.io/molmod/ ========= ================== =============================== version versionsuffix toolchain @@ -17994,6 +18372,7 @@ 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`` ========= ================== =============================== @@ -18079,13 +18458,14 @@ version toolchain Mothur is a single piece of open-source, expandable software to fill the bioinformatics needs of the microbial ecology community. -*homepage*: http://www.mothur.org/ +*homepage*: https://www.mothur.org/ ========== ================== =============== version versionsuffix toolchain ========== ================== =============== ``1.39.5`` ``-Python-2.7.13`` ``intel/2017a`` ``1.41.0`` ``-Python-2.7.15`` ``foss/2018b`` +``1.43.0`` ``-Python-3.7.2`` ``foss/2019a`` ========== ================== =============== @@ -18342,14 +18722,16 @@ MRtrix provides a set of tools to perform diffusion-weighted MR white-matter tra *homepage*: http://www.brain.org.au/software/index.html#mrtrix -=========== ================== =============== -version versionsuffix toolchain -=========== ================== =============== -``0.3.14`` ``-Python-2.7.11`` ``intel/2016a`` -``0.3.15`` ``-Python-2.7.12`` ``intel/2016b`` -``3.0_RC2`` ``-Python-2.7.13`` ``foss/2017a`` -``3.0_RC3`` ``-Python-2.7.14`` ``intel/2018a`` -=========== ================== =============== +=================== ================== =============== +version versionsuffix toolchain +=================== ================== =============== +``0.3.14`` ``-Python-2.7.11`` ``intel/2016a`` +``0.3.15`` ``-Python-2.7.12`` ``intel/2016b`` +``3.0-rc-20191217`` ``-Python-2.7.16`` ``foss/2019b`` +``3.0-rc-20191217`` ``-Python-3.7.4`` ``foss/2019b`` +``3.0_RC2`` ``-Python-2.7.13`` ``foss/2017a`` +``3.0_RC3`` ``-Python-2.7.14`` ``intel/2018a`` +=================== ================== =============== .. _list_software_MSM_237: @@ -18767,7 +19149,7 @@ 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_NCL_221` - :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_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` .. _list_software_NAG_214: @@ -19002,6 +19384,22 @@ version toolchain ======== ================= +.. _list_software_NCIPLOT_537: + +*NCIPLOT* ++++++++++ + +NCIPLOT is a program for revealing non covalent interactions based on the reduced density gradient. + +*homepage*: https://www.lct.jussieu.fr/pagesperso/contrera/index-nci.html + +================ ======================= +version toolchain +================ ======================= +``4.0-20190718`` ``iccifort/2019.5.281`` +================ ======================= + + .. _list_software_NCL_221: *NCL* @@ -19009,17 +19407,33 @@ version toolchain NCL is an interpreted language designed specifically for scientific data analysis and visualization. -*homepage*: http://www.ncl.ucar.edu +*homepage*: https://www.ncl.ucar.edu ========= ================================================= version toolchain ========= ================================================= ``6.4.0`` ``intel/2017a``, ``intel/2017b``, ``intel/2018a`` ``6.5.0`` ``intel/2018a`` -``6.6.2`` ``intel/2018b`` +``6.6.2`` ``foss/2018b``, ``intel/2018b``, ``intel/2019b`` ========= ================================================= +.. _list_software_ncl_317: + +*ncl* ++++++ + +The NEXUS Class Library is a C++ library for parsing NEXUS files. + +*homepage*: http://ncl.sourceforge.net/ + +========== ==================== +version toolchain +========== ==================== +``2.1.18`` ``GCC/8.2.0-2.31.1`` +========== ==================== + + .. _list_software_NCO_224: *NCO* @@ -19086,11 +19500,11 @@ Ncview is a visual browser for netCDF format files. Typically you would use ncvi *homepage*: http://meteora.ucsd.edu/~pierce/ncview_home_page.html -========= ===================================================================================================================================== -version toolchain -========= ===================================================================================================================================== -``2.1.7`` ``foss/2017b``, ``gompi/2019a``, ``intel/2016b``, ``intel/2017a``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b``, ``iomkl/2018b`` -========= ===================================================================================================================================== +========= ====================================================================================================================================================== +version toolchain +========= ====================================================================================================================================================== +``2.1.7`` ``foss/2017b``, ``gompi/2019a``, ``intel/2016b``, ``intel/2017a``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b``, ``intel/2019b``, ``iomkl/2018b`` +========= ====================================================================================================================================================== .. _list_software_nd2reader_887: @@ -19182,7 +19596,7 @@ version versionsuffix toolchain ``4.6.0`` ``foss/2018a``, ``intel/2018a``, ``iomkl/2018a`` ``4.6.1`` ``PGI/18.4-GCC-6.4.0-2.28``, ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b``, ``iomkl/2018b`` ``4.6.2`` ``gompi/2019a``, ``iimpi/2019a`` -``4.7.1`` ``gompi/2019b`` +``4.7.1`` ``gompi/2019b``, ``gompic/2019b``, ``iimpi/2019b``, ``iimpic/2019b`` =========== ================ ========================================================================================================================== @@ -19209,7 +19623,7 @@ version toolchain NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data. -*homepage*: http://www.unidata.ucar.edu/software/netcdf/ +*homepage*: https://www.unidata.ucar.edu/software/netcdf/ ========= ================ ====================================================================================================================================================== version versionsuffix toolchain @@ -19217,6 +19631,7 @@ version versionsuffix toolchain ``4.3.0`` ``foss/2018b``, ``gompi/2019a``, ``iimpi/2019a``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a``, ``intel/2018a``, ``intel/2018b``, ``iomkl/2018b`` ``4.3.0`` ``-HDF5-1.8.18`` ``intel/2017a`` ``4.3.0`` ``-HDF5-1.8.19`` ``intel/2017b`` +``4.3.1`` ``iimpi/2019b`` ========= ================ ====================================================================================================================================================== @@ -19227,7 +19642,7 @@ version versionsuffix toolchain NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data. -*homepage*: http://www.unidata.ucar.edu/software/netcdf/ +*homepage*: https://www.unidata.ucar.edu/software/netcdf/ ========= ================ ==================================================================================================================================================================================================================================================================================================================================== version versionsuffix toolchain @@ -19239,6 +19654,7 @@ 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`` ========= ================ ==================================================================================================================================================================================================================================================================================================================================== @@ -19407,6 +19823,7 @@ version versionsuffix toolchain ``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`` ======== ================== =============================== @@ -19693,7 +20110,7 @@ version versionsuffix toolchain *NLopt* +++++++ -NLopt is a free/open-source library for nonlinear optimization, providing a common interface for a number of different free optimization routines available online as well as original implementations of various other algorithms. +NLopt is a free/open-source library for nonlinear optimization, providing a common interface for a number of different free optimization routines available online as well as original implementations of various other algorithms. *homepage*: http://ab-initio.mit.edu/wiki/index.php/NLopt @@ -19701,7 +20118,7 @@ NLopt is a free/open-source library for nonlinear optimization, providing a co version toolchain ========= =================================================================================================================================================================================================================================================== ``2.4.2`` ``GCC/5.4.0-2.26``, ``GCCcore/7.3.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2017b``, ``foss/2018a``, ``iccifort/2016.3.210-GCC-5.4.0-2.26``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a``, ``intel/2017b``, ``intel/2018a``, ``iomkl/2018a`` -``2.6.1`` ``GCCcore/8.2.0`` +``2.6.1`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` ========= =================================================================================================================================================================================================================================================== @@ -19909,6 +20326,7 @@ version toolchain ``2.0.10`` ``GCC/4.8.4``, ``GCC/4.9.2``, ``GNU/4.9.2-2.25``, ``GNU/4.9.3-2.25`` ``2.0.11`` ``GCC/4.9.3``, ``GCC/4.9.3-2.25``, ``GCC/5.2.0``, ``GCC/5.3.0-2.26``, ``GCC/5.4.0-2.26``, ``GCC/6.1.0-2.27``, ``GCC/6.2.0-2.27``, ``GCC/6.3.0-2.27``, ``GCCcore/4.9.2``, ``GCCcore/4.9.3``, ``GCCcore/5.3.0``, ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``foss/2016a``, ``iccifort/2016.3.210-GCC-4.9.3-2.25``, ``iccifort/2016.3.210-GCC-5.4.0-2.26``, ``intel/2016a``, ``intel/2016b`` ``2.0.12`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` +``2.0.13`` ``GCCcore/9.2.0`` ========== ============================================================================================================================================================================================================================================================================================================================================================================================================================================== @@ -20040,7 +20458,7 @@ 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_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_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` .. _list_software_Oases_507: @@ -20332,13 +20750,15 @@ version toolchain ``4.1`` ``foss/2016b``, ``intel/2017a`` ``5.0`` ``foss/2017b``, ``intel/2017a``, ``intel/2017b`` ``5.0-20180108`` ``foss/2018a``, ``intel/2017b``, ``intel/2018a`` -``6`` ``foss/2018b``, ``intel/2018a`` +``6`` ``foss/2018b``, ``foss/2019b``, ``intel/2018a`` +``7`` ``foss/2019b`` ``v1606+`` ``foss/2018b`` ``v1612+`` ``foss/2018b`` ``v1712`` ``foss/2017b``, ``intel/2017b`` ``v1806`` ``foss/2018b`` ``v1812`` ``foss/2018b`` ``v1906`` ``foss/2019b`` +``v1912`` ``foss/2019b`` ================ ================================================ @@ -20347,17 +20767,18 @@ version toolchain *OpenFOAM-Extend* +++++++++++++++++ -OpenFOAM is a free, open source CFD software package. OpenFOAM has an extensive range of features to solve anything from complex fluid flows involving chemical reactions, turbulence and heat transfer, to solid dynamics and electromagnetics. +OpenFOAM is a free, open source CFD software package. OpenFOAM has an extensive range of features to solve anything from complex fluid flows involving chemical reactions, turbulence and heat transfer, to solid dynamics and electromagnetics. *homepage*: http://www.extend-project.de/ -======= ================================= -version toolchain -======= ================================= -``3.1`` ``gimkl/2.11.5`` -``3.2`` ``gimkl/2.11.5``, ``intel/2016a`` -``4.0`` ``intel/2017a`` -======= ================================= +======= ================== ================================= +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`` +======= ================== ================================= .. _list_software_OpenImageIO_1037: @@ -20437,13 +20858,14 @@ version toolchain OpenMM is a toolkit for molecular simulation. -*homepage*: https://simtk.org/home/openmm +*homepage*: http://openmm.org -========= ================= =============== -version versionsuffix toolchain -========= ================= =============== -``7.1.1`` ``-Python-3.6.3`` ``intel/2017b`` -========= ================= =============== +========= ================= =============================== +version versionsuffix toolchain +========= ================= =============================== +``7.1.1`` ``-Python-3.6.3`` ``intel/2017b`` +``7.4.1`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` +========= ================= =============================== .. _list_software_OpenMolcas_1009: @@ -20504,6 +20926,7 @@ version versionsuffix toolchain ``4.0.0`` ``GCC/8.2.0-2.31.1`` ``4.0.0`` ``-hpcx`` ``GCC/8.2.0-2.31.1`` ``4.0.1`` ``GCC/8.3.0-2.32`` +``4.0.2`` ``GCC/9.2.0-2.32`` ``system`` ``GCC/system-2.29`` ========== ============= ==================================================================================================================== @@ -20572,6 +20995,38 @@ version versionsuffix toolchain ======= =================== ========== +.. _list_software_OpenSlide_899: + +*OpenSlide* ++++++++++++ + +OpenSlide is a C library that provides a simple interface to read whole-slide images (also known as virtual slides). + +*homepage*: https://openslide.org/ + +========= ================= +version toolchain +========= ================= +``3.4.1`` ``GCCcore/8.2.0`` +========= ================= + + +.. _list_software_openslide-python_1682: + +*openslide-python* +++++++++++++++++++ + +OpenSlide Python is a Python interface to the OpenSlide library. + +*homepage*: https://github.com/openslide/openslide-python + +========= ================= +version toolchain +========= ================= +``1.1.1`` ``GCCcore/8.2.0`` +========= ================= + + .. _list_software_OpenSSL_644: *OpenSSL* @@ -20680,6 +21135,7 @@ version versionsuffix toolchain ``4.0.1`` ``-OpenMPI-2.0.2`` ``system`` ``4.1.0`` ``-OpenMPI-3.1.3`` ``system`` ``4.2.0`` ``gompi/2019b`` +``4.2.1`` ``gompi/2019b`` ====================== ================== =============== @@ -20777,11 +21233,12 @@ The ownCloud Desktop Client is a tool to synchronize files from ownCloud Server *homepage*: https://github.com/owncloud/client -========= ============== -version toolchain -========= ============== -``2.4.3`` ``foss/2018b`` -========= ============== +========= ================= +version toolchain +========= ================= +``2.4.3`` ``foss/2018b`` +``2.5.4`` ``GCCcore/8.2.0`` +========= ================= .. _list_software_oxford_asl_1073: @@ -20806,7 +21263,7 @@ 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_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_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` .. _list_software_p11-kit_583: @@ -20992,7 +21449,7 @@ version toolchain Pango is a library for laying out and rendering of text, with an emphasis on internationalization. Pango can be used anywhere that text layout is needed, though most of the work on Pango so far has been done in the context of the GTK+ widget toolkit. Pango forms the core of text and font handling for GTK+-2.x. -*homepage*: http://www.pango.org/ +*homepage*: https://www.pango.org/ =========== ================================== version toolchain @@ -21186,11 +21643,11 @@ 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``, ``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``, ``iimpi/2019a``, ``iimpi/2019b``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b`` +========= ========================================================================================================================================================================================================================================================================= .. _list_software_ParMGridGen_1040: @@ -21202,11 +21659,11 @@ ParMGridGen is an MPI-based parallel library that is based on the serial package *homepage*: http://www-users.cs.umn.edu/~moulitsa/software.html -======= ================================================== -version toolchain -======= ================================================== -``1.0`` ``gimkl/2.11.5``, ``intel/2016a``, ``intel/2017a`` -======= ================================================== +======= =================================================================== +version toolchain +======= =================================================================== +``1.0`` ``gimkl/2.11.5``, ``iimpi/2019b``, ``intel/2016a``, ``intel/2017a`` +======= =================================================================== .. _list_software_pasta_537: @@ -22074,7 +22531,7 @@ version versionsuffix toolchain =============== ================= =================================================== ``5.0.0`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` ``5.3.0.post0`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b`` -``6.0.x.post0`` ``GCCcore/8.2.0`` +``6.0.x.post0`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` =============== ================= =================================================== @@ -22210,6 +22667,7 @@ version toolchain ========== ============================================================================================================================================ ``0.34.0`` ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``foss/2016a``, ``foss/2016b``, ``intel/2016a``, ``intel/2016b`` ``0.38.0`` ``GCCcore/8.2.0`` +``0.38.4`` ``GCCcore/8.3.0`` ========== ============================================================================================================================================ @@ -22441,6 +22899,7 @@ An open-source, interactive graphing library for Python version toolchain ========= =============== ``4.1.0`` ``intel/2019a`` +``4.4.1`` ``intel/2019b`` ========= =============== @@ -22486,6 +22945,7 @@ 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`` ``2.5b`` ``-Python-2.7.14`` ``intel/2018a`` ========= ================== ================================================ @@ -22554,12 +23014,13 @@ Pocl is a portable open source (MIT-licensed) implementation of the OpenCL stand *homepage*: http://portablecl.org -======= ==================== -version toolchain -======= ==================== -``1.2`` ``GCC/7.3.0-2.30`` -``1.3`` ``GCC/8.2.0-2.31.1`` -======= ==================== +======= ================================ +version toolchain +======= ================================ +``1.2`` ``GCC/7.3.0-2.30`` +``1.3`` ``GCC/8.2.0-2.31.1`` +``1.4`` ``GCC/8.3.0``, ``gcccuda/2019b`` +======= ================================ .. _list_software_pomkl_547: @@ -22954,9 +23415,9 @@ version toolchain *PROJ* ++++++ -Program proj is a standard Unix filter function which converts geographic longitude and latitude coordinates into cartesian coordinates +Program proj is a standard Unix filter function which converts geographic longitude and latitude coordinates into cartesian coordinates -*homepage*: http://trac.osgeo.org/proj/ +*homepage*: https://proj.org ========= ================================================================================= version toolchain @@ -22965,6 +23426,7 @@ version toolchain ``4.9.3`` ``foss/2016b``, ``foss/2017b``, ``intel/2016b``, ``intel/2017a``, ``intel/2017b`` ``5.0.0`` ``foss/2018a``, ``foss/2018b``, ``intel/2018a``, ``intel/2018b``, ``iomkl/2018a`` ``6.0.0`` ``GCCcore/8.2.0`` +``6.2.1`` ``GCCcore/8.3.0`` ========= ================================================================================= @@ -22993,15 +23455,15 @@ Prokka is a software tool for the rapid annotation of prokaryotic genomes. *homepage*: https://www.vicbioinformatics.com/software.prokka.shtml -========== ================== =============== -version versionsuffix toolchain -========== ================== =============== -``1.11`` ``-BioPerl-1.7.0`` ``foss/2016b`` -``1.13`` ``-BioPerl-1.7.2`` ``intel/2018a`` -``1.13.4`` ``foss/2018b`` -``1.13.7`` ``gompi/2019a`` -``1.14.5`` ``gompi/2019b`` -========== ================== =============== +========== ================== ================================ +version versionsuffix toolchain +========== ================== ================================ +``1.11`` ``-BioPerl-1.7.0`` ``foss/2016b`` +``1.13`` ``-BioPerl-1.7.2`` ``intel/2018a`` +``1.13.4`` ``foss/2018b`` +``1.13.7`` ``gompi/2019a`` +``1.14.5`` ``gompi/2019a``, ``gompi/2019b`` +========== ================== ================================ .. _list_software_prompt-toolkit_1493: @@ -23489,15 +23951,16 @@ version versionsuffix toolchain *pyBigWig* ++++++++++ -A python extension, written in C, for quick access to bigBed files and access to and creation of bigWig files. +A python extension, written in C, for quick access to bigBed files and access to and creation of bigWig files. *homepage*: https://github.com/deeptools/pyBigWig -========== ================= ============== -version versionsuffix toolchain -========== ================= ============== -``0.3.13`` ``-Python-3.6.6`` ``foss/2018b`` -========== ================= ============== +========== ================= ================= +version versionsuffix toolchain +========== ================= ================= +``0.3.13`` ``-Python-3.6.6`` ``foss/2018b`` +``0.3.17`` ``GCCcore/8.2.0`` +========== ================= ================= .. _list_software_pybind11_744: @@ -23509,12 +23972,13 @@ pybind11 is a lightweight header-only library that exposes C++ types in Python a *homepage*: https://pybind11.readthedocs.io -========= ================= =============== -version versionsuffix toolchain -========= ================= =============== -``2.2.4`` ``-Python-3.6.4`` ``foss/2018a`` -``2.2.4`` ``-Python-3.6.6`` ``intel/2018b`` -========= ================= =============== +========= ================= ================= +version versionsuffix toolchain +========= ================= ================= +``2.2.4`` ``-Python-3.6.4`` ``foss/2018a`` +``2.2.4`` ``-Python-3.6.6`` ``intel/2018b`` +``2.4.3`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` +========= ================= ================= .. _list_software_PyCairo_695: @@ -23526,16 +23990,17 @@ Python bindings for the cairo library *homepage*: https://cairographics.org/pycairo/ -========== ================== =============== -version versionsuffix toolchain -========== ================== =============== -``1.10.0`` ``-Python-2.7.11`` ``intel/2016a`` -``1.16.1`` ``-Python-3.6.3`` ``foss/2017b`` -``1.16.2`` ``-Python-2.7.14`` ``intel/2017b`` -``1.18.0`` ``-Python-2.7.14`` ``intel/2018a`` -``1.18.0`` ``-Python-2.7.15`` ``foss/2018b`` -``1.18.0`` ``-Python-3.6.6`` ``foss/2018b`` -========== ================== =============== +========== ================== ================= +version versionsuffix toolchain +========== ================== ================= +``1.10.0`` ``-Python-2.7.11`` ``intel/2016a`` +``1.16.1`` ``-Python-3.6.3`` ``foss/2017b`` +``1.16.2`` ``-Python-2.7.14`` ``intel/2017b`` +``1.18.0`` ``-Python-2.7.14`` ``intel/2018a`` +``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`` +========== ================== ================= .. _list_software_PyCharm_692: @@ -23551,6 +24016,7 @@ PyCharm Community Edition: Python IDE for Professional Developers version toolchain ============ ========== ``2017.2.3`` ``system`` +``2019.3.1`` ``system`` ============ ========== @@ -23627,15 +24093,16 @@ version versionsuffix toolchain *pydicom* +++++++++ -Read, modify and write DICOM files with python code +Pure python package for DICOM medical file reading and writing. -*homepage*: https://github.com/darcymason/pydicom +*homepage*: https://github.com/pydicom/pydicom -========= ================== =============== -version versionsuffix toolchain -========= ================== =============== -``0.9.9`` ``-Python-2.7.11`` ``intel/2016a`` -========= ================== =============== +========= ================== ================= +version versionsuffix toolchain +========= ================== ================= +``0.9.9`` ``-Python-2.7.11`` ``intel/2016a`` +``1.2.2`` ``GCCcore/8.2.0`` +========= ================== ================= .. _list_software_pydlpoly_893: @@ -23826,16 +24293,17 @@ version versionsuffix toolchain Python Bindings for GLib/GObject/GIO/GTK+ -*homepage*: https://pygobject.readthedocs.io/ +*homepage*: http://www.pygtk.org/ -========== ================== =============== -version versionsuffix toolchain -========== ================== =============== -``2.28.6`` ``-Python-2.7.11`` ``intel/2016a`` -``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`` -========== ================== =============== +========== ================== ================= +version versionsuffix toolchain +========== ================== ================= +``2.28.6`` ``-Python-2.7.11`` ``intel/2016a`` +``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-3.7.2`` ``GCCcore/8.2.0`` +========== ================== ================= .. _list_software_pygrib_653: @@ -24564,6 +25032,22 @@ version versionsuffix toolchain ========== ================== =============== +.. _list_software_pythran_774: + +*pythran* ++++++++++ + +Pythran is an ahead of time compiler for a subset of the Python language, with a focus on scientific computing. It takes a Python module annotated with a few interface description and turns it into a native Python module with the same interface, but (hopefully) faster. + +*homepage*: https://pythran.readthedocs.io + +=============== ================= ============== +version versionsuffix toolchain +=============== ================= ============== +``0.9.4.post1`` ``-Python-3.7.4`` ``foss/2019b`` +=============== ================= ============== + + .. _list_software_PyTorch_713: *PyTorch* @@ -24650,7 +25134,7 @@ 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_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_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: @@ -25010,6 +25494,22 @@ version versionsuffix toolchain ======= ============= ========== +.. _list_software_Qualimap_826: + +*Qualimap* +++++++++++ + +Qualimap 2 is a platform-independent application written in Java and R that provides both a Graphical User Inteface (GUI) and a command-line interface to facilitate the quality control of alignment sequencing data and its derivatives like feature counts. + +*homepage*: http://qualimap.bioinfo.cipf.es/ + +========= ============= ============== +version versionsuffix toolchain +========= ============= ============== +``2.2.1`` ``-R-3.6.0`` ``foss/2019a`` +========= ============= ============== + + .. _list_software_Quandl_613: *Quandl* @@ -25066,6 +25566,7 @@ version versionsuffix toolchain ``4.6.0`` ``-Python-3.5.2`` ``foss/2016b`` ``4.6.3`` ``-Python-3.6.4`` ``foss/2018a`` ``5.0.2`` ``-Python-2.7.15`` ``foss/2018b``, ``foss/2019a`` +``5.0.2`` ``-Python-3.7.2`` ``foss/2019a`` ========= ================== ============================== @@ -25092,13 +25593,14 @@ version toolchain QuickFF is a Python package developed at the Center for Molecular Modeling (CMM) to quickly derive accurate force fields from ab initio calculations. -*homepage*: http://molmod.github.io/QuickFF/ +*homepage*: https://molmod.github.io/QuickFF/ ========= ================== =============== version versionsuffix toolchain ========= ================== =============== ``2.1.4`` ``-Python-2.7.12`` ``intel/2016b`` ``2.2.0`` ``-Python-2.7.14`` ``intel/2017b`` +``2.2.4`` ``-Python-3.7.2`` ``intel/2019a`` ========= ================== =============== @@ -25160,13 +25662,13 @@ The Qwt library contains GUI Components and utility classes which are primarily *homepage*: http://qwt.sourceforge.net/ -========= =============================== -version toolchain -========= =============================== -``6.1.2`` ``intel/2016a`` -``6.1.3`` ``foss/2016b``, ``intel/2016b`` -``6.1.4`` ``GCCcore/8.2.0`` -========= =============================== +========= ==================================================== +version toolchain +========= ==================================================== +``6.1.2`` ``intel/2016a`` +``6.1.3`` ``foss/2016b``, ``intel/2016b`` +``6.1.4`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``foss/2018b`` +========= ==================================================== .. _list_software_QwtPolar_826: @@ -25220,6 +25722,7 @@ version versionsuffix toolchain ``3.5.1`` ``foss/2018b``, ``intel/2018b`` ``3.5.1`` ``-Python-2.7.15`` ``foss/2018b`` ``3.6.0`` ``foss/2019a``, ``fosscuda/2019a``, ``intel/2019a`` +``3.6.2`` ``foss/2019b``, ``fosscuda/2019b`` ========= ================== =================================================== @@ -25593,6 +26096,7 @@ version toolchain ======== ========== ``2.18`` ``system`` ``2.19`` ``system`` +``2.20`` ``system`` ======== ========== @@ -26335,6 +26839,7 @@ version versionsuffix toolchain ``0.12.0`` ``foss/2018b`` ``0.14.1`` ``foss/2018b`` ``0.14.2`` ``gompi/2019a`` +``1.0.0`` ``gompi/2019a`` ========== ================== =============== @@ -26359,14 +26864,15 @@ version toolchain *Sambamba* ++++++++++ -Sambamba is a high performance modern robust and fast tool (and library), written in the D programming language, for working with SAM and BAM files. Current functionality is an important subset of samtools functionality, including view, index, sort, markdup, and depth +Sambamba is a high performance modern robust and fast tool (and library), written in the D programming language, for working with SAM and BAM files. Current functionality is an important subset of samtools functionality, including view, index, sort, markdup, and depth. -*homepage*: http://lomereiter.github.io/sambamba/ +*homepage*: https://lomereiter.github.io/sambamba/ ========= ========== version toolchain ========= ========== ``0.6.6`` ``system`` +``0.7.1`` ``system`` ========= ========== @@ -26428,6 +26934,7 @@ 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`` ========== ================= ======================================================================================================================================= @@ -26664,7 +27171,7 @@ version versionsuffix toolchain ``0.20.0`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b`` ``0.20.2`` ``-Python-2.7.15`` ``foss/2018b`` ``0.20.2`` ``-Python-3.6.6`` ``foss/2018b`` -``0.20.3`` ``foss/2019a``, ``intel/2019a`` +``0.20.3`` ``foss/2019a``, ``fosscuda/2019a``, ``intel/2019a`` ``0.21.3`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` ========== ================================= ======================================================================== @@ -26868,7 +27375,7 @@ version versionsuffix toolchain ``6.0.4`` ``foss/2016a``, ``foss/2016b``, ``foss/2017b``, ``gimkl/2.11.5``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a``, ``intel/2017b``, ``intel/2018a`` ``6.0.4`` ``-64bitint`` ``foss/2017b`` ``6.0.6`` ``foss/2018a``, ``foss/2018b``, ``gompi/2019a``, ``iimpi/2019a``, ``intel/2018a`` -``6.0.9`` ``gompi/2019b`` +``6.0.9`` ``gompi/2019b``, ``iimpi/2019b`` =================== ============= ===================================================================================================================================================== @@ -27137,12 +27644,12 @@ 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`` ``foss/2018a``, ``foss/2018b`` -======= =============================== +======= ==================================================== +version toolchain +======= ==================================================== +``1.2`` ``foss/2016b``, ``intel/2017a`` +``1.3`` ``GCC/8.2.0-2.31.1``, ``foss/2018a``, ``foss/2018b`` +======= ==================================================== .. _list_software_Serf_400: @@ -27785,6 +28292,7 @@ version versionsuffix toolchain ========= ================= =============================== ``5.2.2`` ``-Python-3.6.4`` ``intel/2018a`` ``5.2.4`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` +``5.7.1`` ``-Python-3.7.2`` ``foss/2019a`` ========= ================= =============================== @@ -28744,7 +29252,7 @@ version versionsuffix toolchain SuiteSparse is a collection of libraries manipulate sparse matrices. -*homepage*: http://faculty.cse.tamu.edu/davis/suitesparse.html +*homepage*: https://faculty.cse.tamu.edu/davis/suitesparse.html ========= =================== ================================================================================================= version versionsuffix toolchain @@ -28759,6 +29267,7 @@ 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`` ========= =================== ================================================================================================= @@ -28801,13 +29310,14 @@ version toolchain SUNDIALS: SUite of Nonlinear and DIfferential/ALgebraic Equation Solvers -*homepage*: http://computation.llnl.gov/projects/sundials +*homepage*: https://computation.llnl.gov/projects/sundials ========= ================================================================================================================== version toolchain ========= ================================================================================================================== ``2.6.2`` ``intel/2016b``, ``intel/2018b`` ``2.7.0`` ``foss/2016b``, ``foss/2017b``, ``foss/2018a``, ``intel/2016b``, ``intel/2017a``, ``intel/2017b``, ``intel/2018a`` +``5.1.0`` ``intel/2019b`` ========= ================================================================================================================== @@ -28953,6 +29463,7 @@ version versionsuffix toolchain ``3.0.12`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a``, ``iomkl/2018a`` ``3.0.12`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` ``3.0.12`` ``-Python-3.7.2`` ``GCCcore/8.2.0`` +``4.0.1`` ``GCCcore/8.3.0`` ========== ============================ ================================================================ @@ -29017,7 +29528,7 @@ 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_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_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_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` .. _list_software_tabix_536: @@ -29109,7 +29620,7 @@ version toolchain Intel Threading Building Blocks (Intel TBB) is a widely used, award-winning C++ template library for creating reliable, portable, and scalable parallel applications. Use Intel TBB for a simple and rapid way of developing robust task-based parallel applications that scale to available processor cores, are compatible with multiple environments, and are easier to maintain. Intel TBB is the most proficient way to implement future-proof parallel applications that tap into the power and performance of multicore and manycore hardware platforms. -*homepage*: http://software.intel.com/en-us/articles/intel-tbb/ +*homepage*: https://software.intel.com/en-us/articles/intel-tbb/ ============== ================================================== version toolchain @@ -29144,6 +29655,7 @@ Tbl2asn is a command-line program that automates the creation of sequence recor ============ ============= ========== version versionsuffix toolchain ============ ============= ========== +``25.8`` ``-linux64`` ``system`` ``20180227`` ``-linux64`` ``system`` ============ ============= ========== @@ -29192,15 +29704,16 @@ version toolchain *tcsh* ++++++ -Tcsh is an enhanced, but completely compatible version of the Berkeley UNIX C shell (csh). It is a command language interpreter usable both as an interactive login shell and a shell script command processor. It includes a command-line editor, programmable word completion, spelling correction, a history mechanism, job control and a C-like syntax. +Tcsh is an enhanced, but completely compatible version of the Berkeley UNIX C shell (csh). It is a command language interpreter usable both as an interactive login shell and a shell script command processor. It includes a command-line editor, programmable word completion, spelling correction, a history mechanism, job control and a C-like syntax. -*homepage*: http://www.tcsh.org +*homepage*: https://www.tcsh.org =========== ======================================================= version toolchain =========== ======================================================= ``6.19.00`` ``intel/2016a`` ``6.20.00`` ``GCCcore/5.4.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` +``6.22.02`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` =========== ======================================================= @@ -29266,6 +29779,7 @@ version versionsuffix toolchain ``1.15.0`` ``-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`` ========== ============================= =================================================== @@ -29386,6 +29900,7 @@ version toolchain ``6.4`` ``GCCcore/5.4.0`` ``6.5`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` ``6.6`` ``GCCcore/8.2.0`` +``6.7`` ``GCCcore/8.3.0`` ========= ==================================== @@ -29525,13 +30040,14 @@ version toolchain The `time' command runs another program, then displays information about the resources used by that program, collected by the system while the program was running. -*homepage*: http://www.gnu.org/software/time/ +*homepage*: https://www.gnu.org/software/time/ -======= ========== -version toolchain -======= ========== -``1.7`` ``system`` -======= ========== +======= ================= +version toolchain +======= ================= +``1.7`` ``system`` +``1.9`` ``GCCcore/8.3.0`` +======= ================= .. _list_software_TINKER_461: @@ -29550,6 +30066,22 @@ version toolchain ========= ============== +.. _list_software_TinyDB_554: + +*TinyDB* +++++++++ + +TinyDB is a lightweight document oriented database optimized for your happiness :) It's written in pure Python and has no external dependencies. The target are small apps that would be blown away by a SQL-DB or an external database server. + +*homepage*: https://tinydb.readthedocs.io/ + +========== ================= +version toolchain +========== ================= +``3.15.2`` ``GCCcore/8.3.0`` +========== ================= + + .. _list_software_Tk_191: *Tk* @@ -29688,6 +30220,7 @@ version versionsuffix toolchain ``0.2.0`` ``-Python-3.6.4-CUDA-9.1.85`` ``foss/2018a`` ``0.2.2`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b`` ``0.3.0`` ``-Python-3.7.2`` ``foss/2019a`` +``0.4.2`` ``-Python-3.7.4`` ``fosscuda/2019b`` ========= ============================= ================================== @@ -29809,6 +30342,22 @@ version toolchain ======== =============== +.. _list_software_TreeShrink_1023: + +*TreeShrink* +++++++++++++ + +TreeShrink is an algorithm for detecting abnormally long branches in one or more phylogenetic trees. + +*homepage*: https://github.com/uym2/TreeShrink + +========= ================= ==================== +version versionsuffix toolchain +========= ================= ==================== +``1.3.2`` ``-Python-3.7.2`` ``GCC/8.2.0-2.31.1`` +========= ================= ==================== + + .. _list_software_TRF_236: *TRF* @@ -30192,14 +30741,14 @@ UDUNITS supports conversion of unit specifications between formatted and binary *homepage*: http://www.unidata.ucar.edu/software/udunits/ -========== ===================================================================================================================== -version toolchain -========== ===================================================================================================================== -``2.2.20`` ``foss/2016a``, ``intel/2016b`` -``2.2.24`` ``intel/2017a`` -``2.2.25`` ``foss/2017b``, ``intel/2017b`` -``2.2.26`` ``GCCcore/8.2.0``, ``foss/2018a``, ``foss/2018b``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b``, ``iomkl/2018b`` -========== ===================================================================================================================== +========== ======================================================================================================================================== +version toolchain +========== ======================================================================================================================================== +``2.2.20`` ``foss/2016a``, ``intel/2016b`` +``2.2.24`` ``intel/2017a`` +``2.2.25`` ``foss/2017b``, ``intel/2017b`` +``2.2.26`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``foss/2018a``, ``foss/2018b``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b``, ``iomkl/2018b`` +========== ======================================================================================================================================== .. _list_software_UFL_231: @@ -31265,18 +31814,19 @@ The Worker framework has been developed to help deal with parameter exploration *homepage*: https://github.com/gjbex/worker -========= ================ =============== -version versionsuffix toolchain -========= ================ =============== -``1.6.4`` ``intel/2016a`` -``1.6.5`` ``intel/2016a`` -``1.6.6`` ``intel/2016b`` -``1.6.7`` ``-intel-2016b`` ``system`` -``1.6.7`` ``-intel-2017a`` ``system`` -``1.6.7`` ``-intel-2017b`` ``system`` -``1.6.8`` ``-intel-2018a`` ``system`` -``1.6.8`` ``-intel-2018b`` ``system`` -========= ================ =============== +========== ================ =============== +version versionsuffix toolchain +========== ================ =============== +``1.6.4`` ``intel/2016a`` +``1.6.5`` ``intel/2016a`` +``1.6.6`` ``intel/2016b`` +``1.6.7`` ``-intel-2016b`` ``system`` +``1.6.7`` ``-intel-2017a`` ``system`` +``1.6.7`` ``-intel-2017b`` ``system`` +``1.6.8`` ``-intel-2018a`` ``system`` +``1.6.8`` ``-intel-2018b`` ``system`` +``1.6.11`` ``-intel-2019b`` ``system`` +========== ================ =============== .. _list_software_WPS_250: @@ -31284,7 +31834,7 @@ version versionsuffix toolchain *WPS* +++++ -WRF Preprocessing System (WPS) for WRF. The Weather Research and Forecasting (WRF) Model is a next-generation mesoscale numerical weather prediction system designed to serve both operational forecasting and atmospheric research needs. +WRF Preprocessing System (WPS) for WRF. The Weather Research and Forecasting (WRF) Model is a next-generation mesoscale numerical weather prediction system designed to serve both operational forecasting and atmospheric research needs. *homepage*: http://www.wrf-model.org @@ -31292,6 +31842,9 @@ WRF Preprocessing System (WPS) for WRF. The Weather Research and Forecasting (WR version versionsuffix toolchain ========= ============= =============== ``3.8.0`` ``-dmpar`` ``intel/2016a`` +``4.0.1`` ``-dmpar`` ``intel/2018b`` +``4.0.2`` ``-dmpar`` ``foss/2018b`` +``4.1`` ``-dmpar`` ``intel/2019b`` ========= ============= =============== @@ -31308,6 +31861,9 @@ The Weather Research and Forecasting (WRF) Model is a next-generation mesoscale version versionsuffix toolchain ========= ============= ================================ ``3.8.0`` ``-dmpar`` ``intel/2016a``, ``intel/2016b`` +``4.0.1`` ``-dmpar`` ``intel/2018b`` +``4.0.2`` ``-dmpar`` ``foss/2018b`` +``4.1.3`` ``-dmpar`` ``intel/2019b`` ========= ============= ================================ @@ -31916,15 +32472,15 @@ version toolchain X.org macros utilities. -*homepage*: http://cgit.freedesktop.org/xorg/util/macros +*homepage*: https://cgit.freedesktop.org/xorg/util/macros -========== ================================================================================== -version toolchain -========== ================================================================================== -``1.19.0`` ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``intel/2016a``, ``intel/2016b`` -``1.19.1`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0`` -``1.19.2`` ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` -========== ================================================================================== +========== ============================================================================================= +version toolchain +========== ============================================================================================= +``1.19.0`` ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``intel/2016a``, ``intel/2016b`` +``1.19.1`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0`` +``1.19.2`` ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.2.0`` +========== ============================================================================================= .. _list_software_xprop_569: @@ -31934,7 +32490,7 @@ version toolchain The xprop utility is for displaying window and font properties in an X server. One window or font is selected using the command line arguments or possibly in the case of a window, by clicking on the desired window. A list of properties is then given, possibly with formatting information. -*homepage*: http://www.x.org/wiki/ +*homepage*: https://www.x.org/wiki/ ========= ================= ======================================================================================================================= version versionsuffix toolchain @@ -31942,7 +32498,7 @@ version versionsuffix toolchain ``1.2.2`` ``GCCcore/5.4.0``, ``GCCcore/6.4.0``, ``foss/2016a``, ``foss/2016b``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a`` ``1.2.2`` ``-X11-20180131`` ``GCCcore/6.4.0`` ``1.2.3`` ``GCCcore/7.3.0`` -``1.2.4`` ``GCCcore/8.2.0`` +``1.2.4`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` ========= ================= ======================================================================================================================= @@ -31953,15 +32509,15 @@ version versionsuffix toolchain X protocol and ancillary headers -*homepage*: http://www.freedesktop.org/wiki/Software/xlibs +*homepage*: https://www.freedesktop.org/wiki/Software/xlibs -========== ======================================================= -version toolchain -========== ======================================================= -``7.0.28`` ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a`` -``7.0.29`` ``intel/2016a`` -``7.0.31`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` -========== ======================================================= +========== ========================================================================== +version toolchain +========== ========================================================================== +``7.0.28`` ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a`` +``7.0.29`` ``intel/2016a`` +``7.0.31`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.3.0`` +========== ========================================================================== .. _list_software_XSD_239: @@ -32029,7 +32585,7 @@ version versionsuffix toolchain ``5.2.2`` ``GCC/4.9.2``, ``GCC/5.4.0-2.26``, ``GCCcore/4.9.3``, ``GCCcore/5.4.0``, ``foss/2016.04``, ``foss/2016a``, ``foss/2016b``, ``intel/2016a``, ``intel/2016b`` ``5.2.2`` ``-gettext-0.19.7`` ``foss/2016a``, ``intel/2016a`` ``5.2.3`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``gimkl/2017a`` -``5.2.4`` ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` +``5.2.4`` ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.2.0`` ========= =================== =========================================================================================================================================================== @@ -32082,6 +32638,7 @@ 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`` ==================== ============================== ================================================ @@ -32148,6 +32705,7 @@ version toolchain ========= ================================================= ``0.5.1`` ``intel/2016b``, ``intel/2017a``, ``intel/2017b`` ``0.6.0`` ``intel/2018a``, ``intel/2018b``, ``iomkl/2018b`` +``0.6.2`` ``iimpi/2019b`` ========= ================================================= diff --git a/docs/version-specific/easyblocks.rst b/docs/version-specific/easyblocks.rst index 7709831e..6325e2d8 100644 --- a/docs/version-specific/easyblocks.rst +++ b/docs/version-specific/easyblocks.rst @@ -241,6 +241,7 @@ * EB_UFC * ConfigureMakePythonPackage + * EB_cryptography * EB_EasyBuildMeta * EB_EggLib * EB_libxml2 @@ -361,6 +362,7 @@ * EB_UFC * ConfigureMakePythonPackage + * EB_cryptography * EB_EasyBuildMeta * EB_EggLib * EB_libxml2 diff --git a/docs/version-specific/easyconfig_parameters.rst b/docs/version-specific/easyconfig_parameters.rst index 68a36b9a..b57e93ac 100644 --- a/docs/version-specific/easyconfig_parameters.rst +++ b/docs/version-specific/easyconfig_parameters.rst @@ -126,16 +126,16 @@ license parameters extensions parameters --------------------- -========================== ================================================================================================== ================= -**Parameter name** **Description** **Default value** -========================== ================================================================================================== ================= -``exts_classmap`` Map of extension name to class for handling build and installation. {} -``exts_default_options`` List of default options for extensions {} -``exts_defaultclass`` List of module for and name of the default extension class None -``exts_download_dep_fail`` Fail if downloaded dependencies are detected for extensions False -``exts_filter`` Extension filter details: template for cmd and input to cmd (templates for name, version and src). None -``exts_list`` List with extensions added to the base installation [] -========================== ================================================================================================== ================= +========================== ========================================================================================================== ================= +**Parameter name** **Description** **Default value** +========================== ========================================================================================================== ================= +``exts_classmap`` Map of extension name to class for handling build and installation. {} +``exts_default_options`` List of default options for extensions {} +``exts_defaultclass`` List of module for and name of the default extension class None +``exts_download_dep_fail`` Fail if downloaded dependencies are detected for extensions False +``exts_filter`` Extension filter details: template for cmd and input to cmd (templates for ext_name, ext_version and src). None +``exts_list`` List with extensions added to the base installation [] +========================== ========================================================================================================== ================= modules parameters diff --git a/docs/version-specific/generic_easyblocks.rst b/docs/version-specific/generic_easyblocks.rst index c48b6279..19d45027 100644 --- a/docs/version-specific/generic_easyblocks.rst +++ b/docs/version-specific/generic_easyblocks.rst @@ -167,22 +167,22 @@ Support for configuring build with CMake instead of traditional configure script Extra easyconfig parameters specific to ``CMakeMake`` easyblock --------------------------------------------------------------- -======================== =================================================================================================================================================================================================== ================== -easyconfig parameter description default value -======================== =================================================================================================================================================================================================== ================== -``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`` Value to provide to --build 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`` -``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`` -``srcdir`` Source directory location to provide to cmake command ``None`` -``tar_config_opts`` Override tar settings as determined by configure. ``False`` -======================== =================================================================================================================================================================================================== ================== +======================== ================================================================================================================================================================================================== ================== +easyconfig parameter description default value +======================== ================================================================================================================================================================================================== ================== +``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`` +``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`` +``srcdir`` Source directory location to provide to cmake command ``None`` +``tar_config_opts`` Override tar settings as determined by configure. ``False`` +======================== ================================================================================================================================================================================================== ================== Customised steps in ``CMakeMake`` easyblock ------------------------------------------- @@ -240,24 +240,24 @@ Software configured with CMake but without 'make install' step Extra easyconfig parameters specific to ``CMakeMakeCp`` easyblock ----------------------------------------------------------------- -======================== =================================================================================================================================================================================================== ================== -easyconfig parameter description default value -======================== =================================================================================================================================================================================================== ================== -``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`` Value to provide to --build 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`` -``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`` -``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`` -======================== =================================================================================================================================================================================================== ================== +======================== ================================================================================================================================================================================================== ================== +easyconfig parameter description default value +======================== ================================================================================================================================================================================================== ================== +``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`` +``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`` +``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`` +======================== ================================================================================================================================================================================================== ================== Customised steps in ``CMakeMakeCp`` easyblock --------------------------------------------- @@ -276,22 +276,22 @@ Support for configuring with CMake, building and installing with MesonNinja. Extra easyconfig parameters specific to ``CMakeNinja`` easyblock ---------------------------------------------------------------- -======================== =================================================================================================================================================================================================== ================== -easyconfig parameter description default value -======================== =================================================================================================================================================================================================== ================== -``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`` Value to provide to --build 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`` -``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`` -``srcdir`` Source directory location to provide to cmake command ``None`` -``tar_config_opts`` Override tar settings as determined by configure. ``False`` -======================== =================================================================================================================================================================================================== ================== +======================== ================================================================================================================================================================================================== ================== +easyconfig parameter description default value +======================== ================================================================================================================================================================================================== ================== +``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`` +``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`` +``srcdir`` Source directory location to provide to cmake command ``None`` +``tar_config_opts`` Override tar settings as determined by configure. ``False`` +======================== ================================================================================================================================================================================================== ================== Customised steps in ``CMakeNinja`` easyblock -------------------------------------------- @@ -319,39 +319,39 @@ Build a Python package and module with cmake. Extra easyconfig parameters specific to ``CMakePythonPackage`` easyblock ------------------------------------------------------------------------ -======================== =================================================================================================================================================================================================== ================== -easyconfig parameter description default value -======================== =================================================================================================================================================================================================== ================== -``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`` Value to provide to --build 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`` -``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"`` -``configure_cmd_prefix`` Prefix to be glued before ./configure ``""`` -``download_dep_fail`` Fail if downloaded dependencies are detected ``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"`` -``install_target`` Option to pass to setup.py ``"install"`` -``options`` Dictionary with extension options. ``{}`` -``pip_ignore_installed`` Let pip ignore installed Python packages (i.e. don't remove them) ``True`` -``prefix_opt`` Prefix command line option for configure script ('--prefix=' if None) ``None`` -``req_py_majver`` Required major Python version (only relevant when using system Python) ``2`` -``req_py_minver`` Required minor Python version (only relevant when using system Python) ``6`` -``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`` -``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_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`` -======================== =================================================================================================================================================================================================== ================== +======================== ================================================================================================================================================================================================== ================== +easyconfig parameter description default value +======================== ================================================================================================================================================================================================== ================== +``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`` +``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"`` +``configure_cmd_prefix`` Prefix to be glued before ./configure ``""`` +``download_dep_fail`` Fail if downloaded dependencies are detected ``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"`` +``install_target`` Option to pass to setup.py ``"install"`` +``options`` Dictionary with extension options. ``{}`` +``pip_ignore_installed`` Let pip ignore installed Python packages (i.e. don't remove them) ``True`` +``prefix_opt`` Prefix command line option for configure script ('--prefix=' if None) ``None`` +``req_py_majver`` Required major Python version (only relevant when using system Python) ``None`` +``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`` +``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_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`` +======================== ================================================================================================================================================================================================== ================== Customised steps in ``CMakePythonPackage`` easyblock ---------------------------------------------------- @@ -528,8 +528,8 @@ easyconfig parameter description ``options`` Dictionary with extension options. ``{}`` ``pip_ignore_installed`` Let pip ignore installed Python packages (i.e. don't remove them) ``True`` ``prefix_opt`` Prefix command line option for configure script ('--prefix=' if None) ``None`` -``req_py_majver`` Required major Python version (only relevant when using system Python) ``2`` -``req_py_minver`` Required minor Python version (only relevant when using system Python) ``6`` +``req_py_majver`` Required major Python version (only relevant when using system Python) ``None`` +``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`` ``tar_config_opts`` Override tar settings as determined by configure. ``False`` @@ -627,8 +627,8 @@ easyconfig parameter description ``install_target`` Option to pass to setup.py ``"install"`` ``options`` Dictionary with extension options. ``{}`` ``pip_ignore_installed`` Let pip ignore installed Python packages (i.e. don't remove them) ``True`` -``req_py_majver`` Required major Python version (only relevant when using system Python) ``2`` -``req_py_minver`` Required minor Python version (only relevant when using system Python) ``6`` +``req_py_majver`` Required major Python version (only relevant when using system Python) ``None`` +``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`` ``unpack_sources`` Unpack sources prior to build/install ``True`` @@ -896,8 +896,8 @@ easyconfig parameter description ``install_target`` Option to pass to setup.py ``"install"`` ``options`` Dictionary with extension options. ``{}`` ``pip_ignore_installed`` Let pip ignore installed Python packages (i.e. don't remove them) ``True`` -``req_py_majver`` Required major Python version (only relevant when using system Python) ``2`` -``req_py_minver`` Required minor Python version (only relevant when using system Python) ``6`` +``req_py_majver`` Required major Python version (only relevant when using system Python) ``None`` +``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`` ``unpack_sources`` Unpack sources prior to build/install ``True`` @@ -930,8 +930,8 @@ easyconfig parameter description ``install_target`` Option to pass to setup.py ``"install"`` ``options`` Dictionary with extension options. ``{}`` ``pip_ignore_installed`` Let pip ignore installed Python packages (i.e. don't remove them) ``True`` -``req_py_majver`` Required major Python version (only relevant when using system Python) ``2`` -``req_py_minver`` Required minor Python version (only relevant when using system Python) ``6`` +``req_py_majver`` Required major Python version (only relevant when using system Python) ``None`` +``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`` ``unpack_sources`` Unpack sources prior to build/install ``True`` @@ -1142,7 +1142,7 @@ easyconfig parameter description ``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"`` ``libfabric_configopts`` Configure options for the provided libfabric ``""`` -``libfabric_rebuild`` Rebuild the internal libfabric instead of using the provided binary ``True`` +``libfabric_rebuild`` Try to rebuild internal libfabric instead of using provided binary ``True`` ``license_activation`` License activation type ``"license_server"`` ``m32`` Enable 32-bit toolchain ``False`` ``ofi_internal`` Use internal shipped libfabric instead of external libfabric ``True`` @@ -1217,8 +1217,8 @@ easyconfig parameter description ``install_target`` Option to pass to setup.py ``"install"`` ``options`` Dictionary with extension options. ``{}`` ``pip_ignore_installed`` Let pip ignore installed Python packages (i.e. don't remove them) ``True`` -``req_py_majver`` Required major Python version (only relevant when using system Python) ``2`` -``req_py_minver`` Required minor Python version (only relevant when using system Python) ``6`` +``req_py_majver`` Required major Python version (only relevant when using system Python) ``None`` +``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`` ``unpack_sources`` Unpack sources prior to build/install ``True`` @@ -1251,8 +1251,8 @@ easyconfig parameter description ``install_target`` Option to pass to setup.py ``"install"`` ``options`` Dictionary with extension options. ``{}`` ``pip_ignore_installed`` Let pip ignore installed Python packages (i.e. don't remove them) ``True`` -``req_py_majver`` Required major Python version (only relevant when using system Python) ``2`` -``req_py_minver`` Required minor Python version (only relevant when using system Python) ``6`` +``req_py_majver`` Required major Python version (only relevant when using system Python) ``None`` +``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`` ``unpack_sources`` Unpack sources prior to build/install ``True`` diff --git a/docs/version-specific/help.rst b/docs/version-specific/help.rst index bffd73d8..d7075cdb 100644 --- a/docs/version-specific/help.rst +++ b/docs/version-specific/help.rst @@ -29,119 +29,119 @@ Option flag Option description Debug and logging options (configfile section MAIN) --------------------------------------------------- -=============== ========================================= -Option flag Option description -=============== ========================================= -``-d, --debug`` Enable debug log mode (def False) -``--info`` Enable info log mode (def False) -``--quiet`` Enable quiet/warning log mode (def False) -=============== ========================================= +=============== ============================================== +Option flag Option description +=============== ============================================== +``-d, --debug`` Enable debug log mode (default: False) +``--info`` Enable info log mode (default: False) +``--quiet`` Enable quiet/warning log mode (default: False) +=============== ============================================== Configfile options ------------------ -========================================= ================================================================ -Option flag Option description -========================================= ================================================================ -``--configfiles=CONFIGFILES`` Parse (additional) configfiles (type comma-separated list; def ) -``--ignoreconfigfiles=IGNORECONFIGFILES`` Ignore configfiles (type comma-separated list) -========================================= ================================================================ +========================================= ===================================================================== +Option flag Option description +========================================= ===================================================================== +``--configfiles=CONFIGFILES`` Parse (additional) configfiles (type comma-separated list; default: ) +``--ignoreconfigfiles=IGNORECONFIGFILES`` Ignore configfiles (type comma-separated list) +========================================= ===================================================================== Basic options ------------- -======================================= ================================================================================================================================================================================================================================================== -Option flag Option description -======================================= ================================================================================================================================================================================================================================================== -``--dry-run`` Print build overview incl. dependencies (full paths) (def False) -``-D, --dry-run-short`` Print build overview incl. dependencies (short paths) (def False) -``-x, --extended-dry-run`` Print build environment and (expected) build procedure that will be performed (def False) -``--extended-dry-run-ignore-errors`` Ignore errors that occur during dry run (def True) -``-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 (def False) -``--job`` Submit the build as a job (def False) -``-l, --logtostdout`` Redirect main log to stdout (def False) -``-M, --missing-modules`` Print list of missing modules for dependencies of specified easyconfigs (def False) -``-b BLOCKS, --only-blocks=BLOCKS`` Only build listed blocks (type comma-separated list) -``--rebuild`` Rebuild software, even if module already exists (don't skip OS dependencies checks) (def False) -``-r PATH[:PATH], --robot=PATH[:PATH]`` Enable dependency resolution, using easyconfigs in specified paths (type pathsep-separated list; def ) -``--robot-paths=PATH[:PATH]`` Additional paths to consider by robot for easyconfigs (--robot paths get priority) (type pathsep-separated list; def /home/example/work/easybuild-easyconfigs/easybuild/easyconfigs) -``--search-paths=PATH[:PATH]`` Additional locations to consider in --search (next to --robot and --robot-paths paths) (type pathsep-separated list; def ) -``-k, --skip`` Skip existing software (useful for installing additional packages) (def False) -``-s STOP, --stop=STOP`` Stop the installation after certain step (type choice; def source) (choices: fetch, ready, source, patch, prepare, configure, build, test, install, extensions, postiter, postproc, sanitycheck, cleanup, module, permissions, package, testcases) -``--strict=STRICT`` Set strictness level (type choice; def warn) (choices: ignore, warn, error) -======================================= ================================================================================================================================================================================================================================================== +======================================= ======================================================================================================================================================================================================================================================= +Option flag Option description +======================================= ======================================================================================================================================================================================================================================================= +``--dry-run`` Print build overview incl. dependencies (full paths) (default: False) +``-D, --dry-run-short`` Print build overview incl. dependencies (short paths) (default: False) +``-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) +``--job`` Submit the build as a job (default: False) +``-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) +``--rebuild`` Rebuild software, even if module already exists (don't skip OS dependencies checks) (default: False) +``-r PATH[:PATH], --robot=PATH[:PATH]`` Enable dependency resolution, using easyconfigs in specified paths (type pathsep-separated list; default: ) +``--robot-paths=PATH[:PATH]`` Additional paths to consider by robot for easyconfigs (--robot paths get priority) (type pathsep-separated list; default: /home/example/work/easybuild-easyconfigs/easybuild/easyconfigs) +``--search-paths=PATH[:PATH]`` Additional locations to consider in --search (next to --robot and --robot-paths paths) (type pathsep-separated list; default: ) +``-k, --skip`` Skip existing software (useful for installing additional packages) (default: False) +``-s STOP, --stop=STOP`` Stop the installation after certain step (type choice; default: source) (choices: fetch, ready, source, patch, prepare, configure, build, test, install, extensions, postiter, postproc, sanitycheck, cleanup, module, permissions, package, testcases) +``--strict=STRICT`` Set strictness level (type choice; default: warn) (choices: ignore, warn, error) +======================================= ======================================================================================================================================================================================================================================================= Configuration options --------------------- -================================================================= ============================================================================================================================================================================================================================================================================ -Option flag Option description -================================================================= ============================================================================================================================================================================================================================================================================ -``--avail-module-naming-schemes`` Show all supported module naming schemes (def False) -``--avail-modules-tools`` Show all supported module tools (def False) -``--avail-repositories`` Show all repository types (incl. non-usable) (def False) -``--buildpath=BUILDPATH`` Temporary build path (def /home/example/.local/easybuild/build) -``--containerpath=CONTAINERPATH`` Location where container recipe & image will be stored (def /home/example/.local/easybuild/containers) -``--external-modules-metadata=EXTERNAL-MODULES-METADATA`` List of (glob patterns for) paths to files specifying metadata for external modules (INI format) (type comma-separated list) -``--hooks=HOOKS`` Location of Python module with hook implementations (type str) -``--ignore-dirs=IGNORE-DIRS`` Directory names to ignore when searching for files/dirs (type comma-separated list; def .git,.svn) -``--include-easyblocks=INCLUDE-EASYBLOCKS`` Location(s) of extra or customized easyblocks (type comma-separated list; def ) -``--include-module-naming-schemes=INCLUDE-MODULE-NAMING-SCHEMES`` Location(s) of extra or customized module naming schemes (type comma-separated list; def ) -``--include-toolchains=INCLUDE-TOOLCHAINS`` Location(s) of extra or customized toolchains or toolchain components (type comma-separated list; def ) -``--installpath=INSTALLPATH`` Install path for software and modules (def /home/example/.local/easybuild) -``--installpath-modules=INSTALLPATH-MODULES`` Install path for modules (if None, combine --installpath and --subdir-modules) -``--installpath-software=INSTALLPATH-SOFTWARE`` Install path for software (if None, combine --installpath and --subdir-software) -``--job-backend=JOB-BACKEND`` Backend to use for submitting jobs (type choice; def GC3Pie) (choices: GC3Pie, PbsPython, Slurm) -``--logfile-format=DIR,FORMAT`` Directory name and format of the log file (type comma-separated tuple; def easybuild,easybuild-%(name)s-%(version)s-%(date)s.%(time)s.log) -``--module-depends-on`` Use depends_on (Lmod 7.6.1+) for dependencies in all generated modules (implies recursive unloading of modules). (def False) -``--module-extensions`` Include 'extensions' statement in generated module file (Lua syntax only) (def False) -``--module-naming-scheme=MODULE-NAMING-SCHEME`` Module naming scheme to use (def EasyBuildMNS) -``--module-syntax=MODULE-SYNTAX`` Syntax to be used for module files (type choice; def Lua) (choices: Lua, Tcl) -``--moduleclasses=MODULECLASSES`` Extend supported module classes (For more info on the default classes, use --show-default-moduleclasses) (type comma-separated list; def base,astro,bio,cae,chem,compiler,data,debugger,devel,geo,ide,lang,lib,math,mpi,numlib,perf,quantum,phys,system,toolchain,tools,vis) -``--modules-footer=PATH`` Path to file containing footer to be added to all generated module files -``--modules-header=PATH`` Path to file containing header to be added to all generated module files -``--modules-tool=MODULES-TOOL`` Modules tool to use (type choice; def Lmod) (choices: EnvironmentModules, EnvironmentModulesC, EnvironmentModulesTcl, Lmod) -``--package-naming-scheme=PACKAGE-NAMING-SCHEME`` Packaging naming scheme choice (type choice; def EasyBuildPNS) (choices: EasyBuildPNS) -``--packagepath=PACKAGEPATH`` The destination path for the packages built by package-tool (def /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. (def False) -``--repository=REPOSITORY`` Repository type, using repositorypath (type choice; def FileRepository) (choices: FileRepository, GitRepository, HgRepository) -``--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; def /home/example/.local/easybuild/ebfiles_repo) -``--sourcepath=SOURCEPATH`` Path(s) to where sources should be downloaded (string, colon-separated) (def /home/example/.local/easybuild/sources) -``--subdir-modules=SUBDIR-MODULES`` Installpath subdir for modules (def modules) -``--subdir-software=SUBDIR-SOFTWARE`` Installpath subdir for software (def software) -``--subdir-user-modules=SUBDIR-USER-MODULES`` Base path of user-specific modules relative to their $HOME -``--suffix-modules-path=SUFFIX-MODULES-PATH`` Suffix for module files install path (def all) -``--testoutput=TESTOUTPUT`` Path to where a job should place the output (to be set within jobscript) -``--tmp-logdir=TMP-LOGDIR`` Log directory where temporary log files are stored -``--tmpdir=TMPDIR`` Directory to use for temporary storage -================================================================= ============================================================================================================================================================================================================================================================================ +================================================================= ================================================================================================================================================================================================================================================================================= +Option flag Option description +================================================================= ================================================================================================================================================================================================================================================================================= +``--avail-module-naming-schemes`` Show all supported module naming schemes (default: False) +``--avail-modules-tools`` Show all supported module tools (default: False) +``--avail-repositories`` Show all repository types (incl. non-usable) (default: False) +``--buildpath=BUILDPATH`` Temporary build path (default: /home/example/.local/easybuild/build) +``--containerpath=CONTAINERPATH`` Location where container recipe & image will be stored (default: /home/example/.local/easybuild/containers) +``--external-modules-metadata=EXTERNAL-MODULES-METADATA`` List of (glob patterns for) paths to files specifying metadata for external modules (INI format) (type comma-separated list) +``--hooks=HOOKS`` Location of Python module with hook implementations (type str) +``--ignore-dirs=IGNORE-DIRS`` Directory names to ignore when searching for files/dirs (type comma-separated list; default: .git,.svn) +``--include-easyblocks=INCLUDE-EASYBLOCKS`` Location(s) of extra or customized easyblocks (type comma-separated list; default: ) +``--include-module-naming-schemes=INCLUDE-MODULE-NAMING-SCHEMES`` Location(s) of extra or customized module naming schemes (type comma-separated list; default: ) +``--include-toolchains=INCLUDE-TOOLCHAINS`` Location(s) of extra or customized toolchains or toolchain components (type comma-separated list; default: ) +``--installpath=INSTALLPATH`` Install path for software and modules (default: /home/example/.local/easybuild) +``--installpath-modules=INSTALLPATH-MODULES`` Install path for modules (if None, combine --installpath and --subdir-modules) +``--installpath-software=INSTALLPATH-SOFTWARE`` Install path for software (if None, combine --installpath and --subdir-software) +``--job-backend=JOB-BACKEND`` Backend to use for submitting jobs (type choice; default: GC3Pie) (choices: GC3Pie, PbsPython, Slurm) +``--logfile-format=DIR,FORMAT`` Directory name and format of the log file (type comma-separated tuple; default: easybuild,easybuild-%(name)s-%(version)s-%(date)s.%(time)s.log) +``--module-depends-on`` Use depends_on (Lmod 7.6.1+) for dependencies in all generated modules (implies recursive unloading of modules). (default: False) +``--module-extensions`` Include 'extensions' statement in generated module file (Lua syntax only) (default: False) +``--module-naming-scheme=MODULE-NAMING-SCHEME`` Module naming scheme to use (default: EasyBuildMNS) +``--module-syntax=MODULE-SYNTAX`` Syntax to be used for module files (type choice; default: Lua) (choices: Lua, Tcl) +``--moduleclasses=MODULECLASSES`` Extend supported module classes (For more info on the default classes, use --show-default-moduleclasses) (type comma-separated list; default: base,astro,bio,cae,chem,compiler,data,debugger,devel,geo,ide,lang,lib,math,mpi,numlib,perf,quantum,phys,system,toolchain,tools,vis) +``--modules-footer=PATH`` Path to file containing footer to be added to all generated module files +``--modules-header=PATH`` Path to file containing header to be added to all generated module files +``--modules-tool=MODULES-TOOL`` Modules tool to use (type choice; default: Lmod) (choices: EnvironmentModules, EnvironmentModulesC, EnvironmentModulesTcl, Lmod) +``--package-naming-scheme=PACKAGE-NAMING-SCHEME`` Packaging naming scheme choice (type choice; default: EasyBuildPNS) (choices: EasyBuildPNS) +``--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) +``--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) +``--subdir-software=SUBDIR-SOFTWARE`` Installpath subdir for software (default: software) +``--subdir-user-modules=SUBDIR-USER-MODULES`` Base path of user-specific modules relative to their $HOME +``--suffix-modules-path=SUFFIX-MODULES-PATH`` Suffix for module files install path (default: all) +``--testoutput=TESTOUTPUT`` Path to where a job should place the output (to be set within jobscript) +``--tmp-logdir=TMP-LOGDIR`` Log directory where temporary log files are stored +``--tmpdir=TMPDIR`` Directory to use for temporary storage +================================================================= ================================================================================================================================================================================================================================================================================= Container options ----------------- -=============================================== ====================================================================================================== -Option flag Option description -=============================================== ====================================================================================================== -``--container-build-image`` Build container image (requires sudo privileges!) (def False) -``--container-config=CONFIG`` Configuration for container image (type ) -``--container-image-format=IMAGE-FORMAT`` Container image format (type choice) (choices: ext3, sandbox, sif, squashfs) -``--container-image-name=IMAGE-NAME`` Custom name for container image (defaults to name of easyconfig) -``--container-template-recipe=TEMPLATE-RECIPE`` Template recipe for container image (type ) -``--container-tmpdir=TMPDIR`` Temporary directory where container image is built -``--container-type=TYPE`` Type of container recipe/image to create (type choice; def singularity) (choices: docker, singularity) -=============================================== ====================================================================================================== +=============================================== =========================================================================================================== +Option flag Option description +=============================================== =========================================================================================================== +``--container-build-image`` Build container image (requires sudo privileges!) (default: False) +``--container-config=CONFIG`` Configuration for container image (type ) +``--container-image-format=IMAGE-FORMAT`` Container image format (type choice) (choices: ext3, sandbox, sif, squashfs) +``--container-image-name=IMAGE-NAME`` Custom name for container image (defaults to name of easyconfig) +``--container-template-recipe=TEMPLATE-RECIPE`` Template recipe for container image (type ) +``--container-tmpdir=TMPDIR`` Temporary directory where container image is built +``--container-type=TYPE`` Type of container recipe/image to create (type choice; default: singularity) (choices: docker, singularity) +=============================================== =========================================================================================================== Options for Easyconfigs ----------------------- -=================================================== ================================================================================================================================================================================================================================================ -Option flag Option description -=================================================== ================================================================================================================================================================================================================================================ -``--fix-deprecated-easyconfigs`` Fix use of deprecated functionality in specified easyconfig files. (def False) -``--inject-checksums=INJECT-CHECKSUMS`` Inject checksums of specified type for sources/patches into easyconfig file(s) (type choice; def 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; def warn) (choices: error, log, warn) -=================================================== ================================================================================================================================================================================================================================================ +=================================================== ===================================================================================================================================================================================================================================================== +Option flag Option description +=================================================== ===================================================================================================================================================================================================================================================== +``--fix-deprecated-easyconfigs`` Fix use of deprecated functionality in specified easyconfig files. (default: False) +``--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) +=================================================== ===================================================================================================================================================================================================================================================== GitHub integration options @@ -149,72 +149,73 @@ GitHub integration options ======================================================= ================================================================================================================================ Option flag Option description ======================================================= ================================================================================================================================ -``--check-contrib`` Runs checks to see whether the given easyconfigs are ready to be contributed back (def False) -``--check-github`` Check status of GitHub integration, and report back (def False) -``--check-style`` Run a style check on the given easyconfigs (def False) -``--cleanup-easyconfigs`` Clean up easyconfig files for pull request (def True) +``--check-contrib`` Runs checks to see whether the given easyconfigs are ready to be contributed back (default: False) +``--check-github`` Check status of GitHub integration, and report back (default: False) +``--check-style`` Run a style check on the given easyconfigs (default: False) +``--cleanup-easyconfigs`` Clean up easyconfig files for pull request (default: True; disable with --disable-cleanup-easyconfigs) ``--close-pr=PR#`` Close pull request (type ) ``--close-pr-msg=CLOSE-PR-MSG`` Custom close message for pull request closed with --close-pr; (type ) ``--close-pr-reasons=CLOSE-PR-REASONS`` Close reason for pull request closed with --close-pr; supported values: archived, inactive, obsolete, retest (type ) -``--dump-test-report=DUMP-TEST-REPORT`` Dump test report to specified path (def test_report.md) +``--dump-test-report=DUMP-TEST-REPORT`` Dump test report to specified path (default: test_report.md) ``--from-pr=PR#`` Obtain easyconfigs from specified PR (type ) ``--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 ) -``--install-github-token`` Install GitHub token (requires --github-user) (def False) -``--list-prs=STATE,ORDER,DIRECTION`` List pull requests (type ; def open,created,desc) +``--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 ) -``--new-branch-github`` Create new branch in GitHub in preparation for a PR (def False) -``--new-pr`` Open a new pull request (def False) +``--new-branch-github`` Create new branch in GitHub in preparation for a PR (default: False) +``--new-pr`` Open a new pull request (default: False) ``--new-pr-from-branch=NEW-PR-FROM-BRANCH`` Open a new pull request from branch in GitHub (type ) ``--pr-branch-name=PR-BRANCH-NAME`` Branch name to use for new PRs; '_new_pr_' if unspecified (type ) ``--pr-commit-msg=PR-COMMIT-MSG`` Commit message for new/updated pull request created with --new-pr (type ) ``--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 ; def easybuilders) -``--pr-target-branch=PR-TARGET-BRANCH`` Target branch for new PRs (type ; def develop) -``--pr-target-repo=PR-TARGET-REPO`` Target repository for new/updating PRs (type ; def easybuild-easyconfigs) +``--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-title=PR-TITLE`` Title for new pull request created with --new-pr (type ) -``--preview-pr`` Preview a new pull request (def False) +``--preview-pr`` Preview a new pull request (default: False) ``--review-pr=PR#`` Review specified pull request (type ) ``--sync-branch-with-develop=SYNC-BRANCH-WITH-DEVELOP`` Sync branch with current 'develop' branch (type ) ``--sync-pr-with-develop=PR#`` Sync pull request with current 'develop' branch (type ) ``--test-report-env-filter=TEST-REPORT-ENV-FILTER`` Regex used to filter out variables in environment dump of test report ``--update-branch-github=UPDATE-BRANCH-GITHUB`` Update specified branch in GitHub (type ) ``--update-pr=PR#`` Update an existing pull request (type ) -``-u, --upload-test-report`` Upload full test report as a gist on GitHub (def False) +``-u, --upload-test-report`` Upload full test report as a gist on GitHub (default: False) ======================================================= ================================================================================================================================ Informative options ------------------- -===================================================== =========================================================================================== -Option flag Option description -===================================================== =========================================================================================== -``--avail-cfgfile-constants`` Show all constants that can be used in configuration files (def False) -``--avail-easyconfig-constants`` Show all constants that can be used in easyconfigs (def False) -``--avail-easyconfig-licenses`` Show all license constants that can be used in easyconfigs (def False) -``-a, --avail-easyconfig-params`` Show all easyconfig parameters (include easyblock-specific ones by using -e) (def False) -``--avail-easyconfig-templates`` Show all template names and template constants that can be used in easyconfigs. (def False) -``--avail-hooks`` Show list of known hooks (def False) -``--avail-toolchain-opts=AVAIL-TOOLCHAIN-OPTS`` Show options for toolchain (type str) -``--check-conflicts`` Check for version conflicts in dependency graphs (def False) -``--dep-graph=depgraph.`` Create dependency graph -``--dump-env-script`` Dump source script to set up build environment based on toolchain/dependencies (def False) -``--last-log`` Print location to EasyBuild log file of last (failed) session (def False) -``--list-easyblocks=LIST-EASYBLOCKS`` Show list of available easyblocks (type choice; def simple) (choices: simple, detailed) -``--list-installed-software=LIST-INSTALLED-SOFTWARE`` Show list of installed software (type choice; def simple) (choices: simple, detailed) -``--list-software=LIST-SOFTWARE`` Show list of supported software (type choice; def simple) (choices: simple, detailed) -``--list-toolchains`` Show list of known toolchains (def False) -``--search=REGEX`` Search for easyconfig files in the robot search path, print full paths -``--search-filename=REGEX`` Search for easyconfig files in the robot search path, print only filenames -``-S REGEX, --search-short=REGEX`` Search for easyconfig files in the robot search path, print short paths -``--show-config`` Show current EasyBuild configuration (only non-default + selected settings) (def False) -``--show-default-configfiles`` Show list of default config files (def False) -``--show-default-moduleclasses`` Show default module classes with description (def False) -``--show-full-config`` Show current EasyBuild configuration (all settings) (def False) -``--show-system-info`` Show system information relevant to EasyBuild (def False) -``--terse`` Terse output (machine-readable) (def False) -===================================================== =========================================================================================== +===================================================== ================================================================================================ +Option flag Option description +===================================================== ================================================================================================ +``--avail-cfgfile-constants`` Show all constants that can be used in configuration files (default: False) +``--avail-easyconfig-constants`` Show all constants that can be used in easyconfigs (default: False) +``--avail-easyconfig-licenses`` Show all license constants that can be used in easyconfigs (default: False) +``-a, --avail-easyconfig-params`` Show all easyconfig parameters (include easyblock-specific ones by using -e) (default: False) +``--avail-easyconfig-templates`` Show all template names and template constants that can be used in easyconfigs. (default: False) +``--avail-hooks`` Show list of known hooks (default: False) +``--avail-toolchain-opts=AVAIL-TOOLCHAIN-OPTS`` Show options for toolchain (type str) +``--check-conflicts`` Check for version conflicts in dependency graphs (default: False) +``--dep-graph=depgraph.`` Create dependency graph +``--dump-env-script`` Dump source script to set up build environment based on toolchain/dependencies (default: False) +``--last-log`` Print location to EasyBuild log file of last (failed) session (default: False) +``--list-easyblocks=LIST-EASYBLOCKS`` Show list of available easyblocks (type choice; default: simple) (choices: simple, detailed) +``--list-installed-software=LIST-INSTALLED-SOFTWARE`` Show list of installed software (type choice; default: simple) (choices: simple, detailed) +``--list-software=LIST-SOFTWARE`` Show list of supported software (type choice; default: simple) (choices: simple, detailed) +``--list-toolchains`` Show list of known toolchains (default: False) +``--search=REGEX`` Search for easyconfig files in the robot search path, print full paths +``--search-filename=REGEX`` Search for easyconfig files in the robot search path, print only filenames +``-S REGEX, --search-short=REGEX`` Search for easyconfig files in the robot search path, print short paths +``--show-config`` Show current EasyBuild configuration (only non-default + selected settings) (default: False) +``--show-default-configfiles`` Show list of default config files (default: False) +``--show-default-moduleclasses`` Show default module classes with description (default: False) +``--show-ec`` Show contents of specified easyconfig(s) (default: False) +``--show-full-config`` Show current EasyBuild configuration (all settings) (default: False) +``--show-system-info`` Show system information relevant to EasyBuild (default: False) +``--terse`` Terse output (machine-readable) (default: False) +===================================================== ================================================================================================ Options for job backend @@ -225,10 +226,10 @@ Option flag Option description ``--job-backend-config=BACKEND-CONFIG`` Configuration file for job backend ``--job-cores=CORES`` Number of cores to request per job (type int) ``--job-deps-type=DEPS-TYPE`` Type of dependency to set between jobs (default depends on job backend) (type choice) (choices: abort_on_error, always_run) -``--job-max-jobs=MAX-JOBS`` Maximum number of concurrent jobs (queued and running, 0 = unlimited) (type int; def 0) -``--job-max-walltime=MAX-WALLTIME`` Maximum walltime for jobs (in hours) (type int; def 24) -``--job-output-dir=OUTPUT-DIR`` Output directory for jobs (default: current directory) (def /Volumes/work/easybuild/docs) -``--job-polling-interval=POLLING-INTERVAL`` Interval between polls for status of jobs (in seconds) (type ; def 30.0) +``--job-max-jobs=MAX-JOBS`` Maximum number of concurrent jobs (queued and running, 0 = unlimited) (type int; default: 0) +``--job-max-walltime=MAX-WALLTIME`` Maximum walltime for jobs (in hours) (type int; default: 24) +``--job-output-dir=OUTPUT-DIR`` Output directory for jobs (default: current directory) (default: /Volumes/work/easybuild/docs) +``--job-polling-interval=POLLING-INTERVAL`` Interval between polls for status of jobs (in seconds) (type ; default: 30.0) ``--job-target-resource=TARGET-RESOURCE`` Target resource for jobs =========================================== =========================================================================================================================== @@ -238,85 +239,87 @@ Override options ========================================================================= ================================================================================================================================================================================== Option flag Option description ========================================================================= ================================================================================================================================================================================== -``--add-dummy-to-minimal-toolchains`` Include dummy toolchain in minimal toolchain searches [DEPRECATED, use --add-system-to-minimal-toolchains instead!) (def False) -``--add-system-to-minimal-toolchains`` Include system toolchain in minimal toolchain searches (def False) -``--allow-loaded-modules=ALLOW-LOADED-MODULES`` List of software names for which to allow loaded modules in initial environment (type comma-separated list; def EasyBuild) -``--allow-modules-tool-mismatch`` Allow mismatch of modules tool and definition of 'module' function (def False) -``--allow-use-as-root-and-accept-consequences`` Allow using of EasyBuild as root (NOT RECOMMENDED!) (def False) +``--add-dummy-to-minimal-toolchains`` Include dummy toolchain in minimal toolchain searches [DEPRECATED, use --add-system-to-minimal-toolchains instead!) (default: False) +``--add-system-to-minimal-toolchains`` Include system toolchain in minimal toolchain searches (default: False) +``--allow-loaded-modules=ALLOW-LOADED-MODULES`` List of software names for which to allow loaded modules in initial environment (type comma-separated list; default: EasyBuild) +``--allow-modules-tool-mismatch`` Allow mismatch of modules tool and definition of 'module' function (default: False) +``--allow-use-as-root-and-accept-consequences`` Allow using of EasyBuild as root (NOT RECOMMENDED!) (default: False) ``--backup-modules`` Back up an existing module file, if any. Only works when using --module-only -``--check-ebroot-env-vars=CHECK-EBROOT-ENV-VARS`` Action to take when defined $EBROOT* environment variables are found for which there is no matching loaded module; supported values: error, ignore, unset, warn (def warn) -``--cleanup-builddir`` Cleanup build dir after successful installation. (def True) -``--cleanup-tmpdir`` Cleanup tmp dir after successful run. (def True) -``--color=WHEN`` Colorize output (type choice; def auto) (choices: auto, always, never) -``--consider-archived-easyconfigs`` Also consider archived easyconfigs (def False) -``-C, --containerize`` Generate container recipe/image (def False) -``--debug-lmod`` Run Lmod modules tool commands in debug module (def False) -``--default-opt-level=DEFAULT-OPT-LEVEL`` Specify default optimisation level (type choice; def defaultopt) (choices: noopt, lowopt, defaultopt, opt) +``--check-ebroot-env-vars=CHECK-EBROOT-ENV-VARS`` Action to take when defined $EBROOT* environment variables are found for which there is no matching loaded module; supported values: error, ignore, unset, warn (default: warn) +``--cleanup-builddir`` Cleanup build dir after successful installation. (default: True; disable with --disable-cleanup-builddir) +``--cleanup-tmpdir`` Cleanup tmp dir after successful run. (default: True; disable with --disable-cleanup-tmpdir) +``--color=WHEN`` Colorize output (type choice; default: auto) (choices: auto, always, never) +``--consider-archived-easyconfigs`` Also consider archived easyconfigs (default: False) +``-C, --containerize`` Generate container recipe/image (default: False) +``--copy-ec`` Copy specified easyconfig(s) to specified location (default: False) +``--cuda-compute-capabilities=CUDA-COMPUTE-CAPABILITIES`` List of CUDA compute capabilities to use when building GPU software (type comma-separated list) +``--debug-lmod`` Run Lmod modules tool commands in debug module (default: False) +``--default-opt-level=DEFAULT-OPT-LEVEL`` Specify default optimisation level (type choice; default: defaultopt) (choices: noopt, lowopt, defaultopt, opt) ``--deprecated=DEPRECATED`` Run pretending to be (future) version, to test removal of deprecated code. -``--detect-loaded-modules=DETECT-LOADED-MODULES`` Detect loaded EasyBuild-generated modules, act accordingly; supported values: error, ignore, purge, unload, warn (def warn) -``--devel`` Enable including of development log messages (def False) +``--detect-loaded-modules=DETECT-LOADED-MODULES`` Detect loaded EasyBuild-generated modules, act accordingly; supported values: error, ignore, purge, unload, warn (default: warn) +``--devel`` Enable including of development log messages (default: False) ``--download-timeout=DOWNLOAD-TIMEOUT`` Timeout for initiating downloads (in seconds) (type ) -``--dump-autopep8`` Reformat easyconfigs using autopep8 when dumping them (def False) +``--dump-autopep8`` Reformat easyconfigs using autopep8 when dumping them (default: False) ``-e CLASS, --easyblock=CLASS`` easyblock to use for processing the spec file or dumping the options -``--enforce-checksums`` Enforce availability of checksums for all sources/patches, so they can be verified (def False) -``--experimental`` Allow experimental code (with behaviour that can be changed/removed at any given time). (def False) +``--enforce-checksums`` Enforce availability of checksums for all sources/patches, so they can be verified (default: False) +``--experimental`` Allow experimental code (with behaviour that can be changed/removed at any given time). (default: False) ``--extra-modules=EXTRA-MODULES`` List of extra modules to load after setting up the build environment (type comma-separated list) -``--fetch`` Allow downloading sources ignoring OS and modules tool dependencies, implies --stop=fetch, --ignore-osdeps and ignore modules tool (def False) +``--fetch`` Allow downloading sources ignoring OS and modules tool dependencies, implies --stop=fetch, --ignore-osdeps and ignore modules tool (default: False) ``--filter-deps=FILTER-DEPS`` List of dependencies that you do *not* want to install with EasyBuild, because equivalent OS packages are installed. (e.g. --filter-deps=zlib,ncurses) (type comma-separated list) ``--filter-env-vars=FILTER-ENV-VARS`` List of names of environment variables that should *not* be defined/updated by module files generated by EasyBuild (type comma-separated list) -``--fixed-installdir-naming-scheme`` Use fixed naming scheme for installation directories (def True) -``--force-download=FORCE-DOWNLOAD`` Force re-downloading of sources and/or patches, even if they are available already in source path (type choice; def sources) (choices: all, patches, sources) +``--fixed-installdir-naming-scheme`` Use fixed naming scheme for installation directories (default: True; disable with --disable-fixed-installdir-naming-scheme) +``--force-download=FORCE-DOWNLOAD`` Force re-downloading of sources and/or patches, even if they are available already in source path (type choice; default: sources) (choices: all, patches, sources) ``--group=GROUP`` Group to be used for software installations (only verified, not set) -``--group-writable-installdir`` Enable group write permissions on installation directory after installation (def False) -``--hidden`` Install 'hidden' module file(s) by prefixing their version with '.' (def False) +``--group-writable-installdir`` Enable group write permissions on installation directory after installation (default: False) +``--hidden`` Install 'hidden' module file(s) by prefixing their version with '.' (default: False) ``--hide-deps=HIDE-DEPS`` Comma separated list of dependencies that you want automatically hidden, (e.g. --hide-deps=zlib,ncurses) (type comma-separated list) ``--hide-toolchains=HIDE-TOOLCHAINS`` Comma separated list of toolchains that you want automatically hidden, (e.g. --hide-toolchains=GCCcore) (type comma-separated list) -``--ignore-checksums`` Ignore failing checksum verification (def False) -``--ignore-osdeps`` Ignore any listed OS dependencies (def False) -``--install-latest-eb-release`` Install latest known version of easybuild (def False) -``--lib64-fallback-sanity-check`` Fallback in sanity check to lib64/ equivalent for missing libraries (def True) -``--max-fail-ratio-adjust-permissions=MAX-FAIL-RATIO-ADJUST-PERMISSIONS`` Maximum ratio for failures to allow when adjusting permissions (type float; def 0.5) -``--minimal-toolchains`` Use minimal toolchain when resolving dependencies (def False) -``--module-only`` Only generate module file(s); skip all steps except for module, prepare, ready, postiter, sanitycheck (def False) -``--modules-tool-version-check`` Check version of modules tool being used (def True) +``--ignore-checksums`` Ignore failing checksum verification (default: False) +``--ignore-osdeps`` Ignore any listed OS dependencies (default: False) +``--install-latest-eb-release`` Install latest known version of easybuild (default: False) +``--lib64-fallback-sanity-check`` Fallback in sanity check to lib64/ equivalent for missing libraries (default: True; disable with --disable-lib64-fallback-sanity-check) +``--max-fail-ratio-adjust-permissions=MAX-FAIL-RATIO-ADJUST-PERMISSIONS`` Maximum ratio for failures to allow when adjusting permissions (type float; default: 0.5) +``--minimal-toolchains`` Use minimal toolchain when resolving dependencies (default: False) +``--module-only`` Only generate module file(s); skip all steps except for module, prepare, ready, postiter, sanitycheck (default: False) +``--modules-tool-version-check`` Check version of modules tool being used (default: True; disable with --disable-modules-tool-version-check) ``--mpi-cmd-template=MPI-CMD-TEMPLATE`` Template for MPI commands (template keys: %(nr_ranks)s, %(cmd)s) -``--mpi-tests`` Run MPI tests (when relevant) (def True) +``--mpi-tests`` Run MPI tests (when relevant) (default: True; disable with --disable-mpi-tests) ``--optarch=OPTARCH`` Set architecture optimization, overriding native architecture optimizations -``--output-format=OUTPUT-FORMAT`` Set output format (type choice; def txt) (choices: txt, rst) +``--output-format=OUTPUT-FORMAT`` Set output format (type choice; default: txt) (choices: txt, rst) ``--parallel=PARALLEL`` Specify (maximum) level of parallellism used during build procedure (type int) -``--pre-create-installdir`` Create installation directory before submitting build jobs (def True) -``-p, --pretend`` Does the build/installation in a test directory located in $HOME/easybuildinstall (def False) -``--read-only-installdir`` Set read-only permissions on installation directory after installation (def False) -``--remove-ghost-install-dirs`` Remove ghost installation directories when --force or --rebuild is used, rather than just warning about them (def False) -``--rpath`` Enable use of RPATH for linking with libraries (def False) +``--pre-create-installdir`` Create installation directory before submitting build jobs (default: True; disable with --disable-pre-create-installdir) +``-p, --pretend`` Does the build/installation in a test directory located in $HOME/easybuildinstall (default: False) +``--read-only-installdir`` Set read-only permissions on installation directory after installation (default: False) +``--remove-ghost-install-dirs`` Remove ghost installation directories when --force or --rebuild is used, rather than just warning about them (default: False) +``--rpath`` Enable use of RPATH for linking with libraries (default: False) ``--rpath-filter=RPATH-FILTER`` List of regex patterns to use for filtering out RPATH paths (type comma-separated list) -``--set-default-module`` Set the generated module as default (def False) -``--set-gid-bit`` Set group ID bit on newly created directories (def False) +``--set-default-module`` Set the generated module as default (default: False) +``--set-gid-bit`` Set group ID bit on newly created directories (default: False) ``--silence-deprecation-warnings=SILENCE-DEPRECATION-WARNINGS`` Silence specified deprecation warnings (type comma-separated list) -``-t, --skip-test-cases`` Skip running test cases (def False) -``--sticky-bit`` Set sticky bit on newly created directories (def False) -``-T, --trace`` Provide more information in output to stdout on progress (def False) +``-t, --skip-test-cases`` Skip running test cases (default: False) +``--sticky-bit`` Set sticky bit on newly created directories (default: False) +``-T, --trace`` Provide more information in output to stdout on progress (default: False) ``--umask=UMASK`` umask to use (e.g. '022'); non-user write permissions on install directories are removed -``--update-modules-tool-cache`` Update modules tool cache file(s) after generating module file (def False) -``--use-ccache=PATH`` Enable use of ccache to speed up compilation, with specified cache dir (type ; def False) -``--use-existing-modules`` Use existing modules when resolving dependencies with minimal toolchains (def False) -``--use-f90cache=PATH`` Enable use of f90cache to speed up compilation, with specified cache dir (type ; def False) -``--verify-easyconfig-filenames`` Verify whether filename of specified easyconfigs matches with contents (def False) -``--zip-logs=ZIP-LOGS`` Zip logs that are copied to install directory, using specified command (def gzip) +``--update-modules-tool-cache`` Update modules tool cache file(s) after generating module file (default: False) +``--use-ccache=PATH`` Enable use of ccache to speed up compilation, with specified cache dir (type ; default: False) +``--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) +``--zip-logs=ZIP-LOGS`` Zip logs that are copied to install directory, using specified command (default: gzip) ========================================================================= ================================================================================================================================================================================== Package options --------------- -=============================================== ========================================= -Option flag Option description -=============================================== ========================================= -``--package`` Enabling packaging (def False) -``--package-release=PACKAGE-RELEASE`` Package release iteration number (def 1) -``--package-tool=PACKAGE-TOOL`` Packaging tool to use (def fpm) -``--package-tool-options=PACKAGE-TOOL-OPTIONS`` Extra options for packaging tool (def '') -``--package-type=PACKAGE-TYPE`` Type of package to generate (def rpm) -=============================================== ========================================= +=============================================== ============================================== +Option flag Option description +=============================================== ============================================== +``--package`` Enabling packaging (default: False) +``--package-release=PACKAGE-RELEASE`` Package release iteration number (default: 1) +``--package-tool=PACKAGE-TOOL`` Packaging tool to use (default: fpm) +``--package-tool-options=PACKAGE-TOOL-OPTIONS`` Extra options for packaging tool (default: '') +``--package-type=PACKAGE-TYPE`` Type of package to generate (default: rpm) +=============================================== ============================================== Regression test options @@ -325,9 +328,9 @@ Regression test options Option flag Option description ============================ ========================================================================== ``--aggregate-regtest=DIR`` Collect all the xmls inside the given directory and generate a single file -``--regtest`` Enable regression test mode (def False) +``--regtest`` Enable regression test mode (default: False) ``--regtest-output-dir=DIR`` Set output directory for test-run -``--sequential`` Specify this option if you want to prevent parallel build (def False) +``--sequential`` Specify this option if you want to prevent parallel build (default: False) ============================ ========================================================================== @@ -337,7 +340,7 @@ Software search and build options Option flag Option description =================================== =================================================================================================================================================================== ``--amend=VAR=VALUE[,VALUE]`` Specify additional search and build parameters (can be used multiple times); for example: versionprefix=foo or patches=one.patch,two.patch) -``--map-toolchains`` Enable mapping of (sub)toolchains when --try-toolchain(-version) is used (def True) +``--map-toolchains`` Enable mapping of (sub)toolchains when --try-toolchain(-version) is used (default: True; disable with --disable-map-toolchains) ``--software=NAME,VERSION`` Search and build software with given name and version (type comma-separated list) ``--software-name=NAME`` Search and build software with given name ``--software-version=VERSION`` Search and build software with given version diff --git a/setup.py b/setup.py index 739b9420..8fa7e12e 100644 --- a/setup.py +++ b/setup.py @@ -36,7 +36,7 @@ # 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 = '4.1.0' +VERSION = '4.1.1' # Utility function to read README file