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tool_dependencies.xml
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tool_dependencies.xml
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<?xml version="1.0"?>
<tool_dependency>
<package name="R" version="3.1.2">
<repository changeset_revision="9f2fddb9d6e2" name="package_r_3_1_2"
owner="iuc" prior_installation_required="True"
toolshed="http://toolshed.g2.bx.psu.edu" />
</package>
<package name="readline" version="6.2">
<repository changeset_revision="52d6f646b3b5" name="package_readline_6_2"
owner="iuc" prior_installation_required="True"
toolshed="http://toolshed.g2.bx.psu.edu" />
</package>
<package name="rpy2" version="2.3.10">
<install version="1.0">
<actions>
<action type="download_by_url">
https://pypi.python.org/packages/source/r/rpy2/rpy2-2.3.10.tar.gz
</action>
<action type="set_environment_for_install">
<repository changeset_revision="52d6f646b3b5" name="package_readline_6_2"
owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu">
<package name="readline" version="6.2" />
</repository>
<repository changeset_revision="9f2fddb9d6e2" name="package_r_3_1_2"
owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu">
<package name="R" version="3.1.2" />
</repository>
</action>
<action type="shell_command">
export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &&
export LDFLAGS="-L$READLINE_LIB_PATH -lreadline" &&
export CPPFLAGS="-I$READLINE_INCLUDE_PATH" &&
python setup.py build --r-home $R_HOME --r-home-lib $R_HOME/lib install --install-lib $INSTALL_DIR/lib/python
</action>
<action type="set_environment">
<environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>
<environment_variable action="append_to" name="LD_LIBRARY_PATH">$ENV[READLINE_LIB_PATH]</environment_variable>
<environment_variable action="append_to" name="LD_LIBRARY_PATH">$ENV[RHOME]/lib</environment_variable>
<environment_variable action="append_to" name="LD_LIBRARY_PATH">$ENV[R_ROOT_DIR]/lib</environment_variable>
</action>
</actions>
</install>
<readme>rpy2 is a redesign and rewrite of rpy. It is providing a low-level interface to R,
a proposed high-level interface, including wrappers to graphical libraries,
as well as R-like structures and functions.
http://rpy.sourceforge.net/rpy2.html
</readme>
</package>
<package name="riboseqr_wrapper_deps" version="0.4.0">
<install version="1.0">
<actions>
<action type="setup_r_environment">
<repository changeset_revision="9f2fddb9d6e2" name="package_r_3_1_2"
owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu">
<package name="R" version="3.1.2" />
</repository>
<package>
https://github.com/vimalkumarvelayudhan/riboseqr_wrapper_deps/raw/master/0.4.0/BiocGenerics_0.12.1.tar.gz?raw=true
</package>
<package>
https://github.com/vimalkumarvelayudhan/riboseqr_wrapper_deps/raw/master/0.4.0/S4Vectors_0.4.0.tar.gz?raw=true
</package>
<package>
https://github.com/vimalkumarvelayudhan/riboseqr_wrapper_deps/raw/master/0.4.0/IRanges_2.0.1.tar.gz?raw=true
</package>
<package>
https://github.com/vimalkumarvelayudhan/riboseqr_wrapper_deps/raw/master/0.4.0/GenomeInfoDb_1.2.5.tar.gz?raw=true
</package>
<package>
https://github.com/vimalkumarvelayudhan/riboseqr_wrapper_deps/raw/master/0.4.0/XVector_0.6.0.tar.gz?raw=true
</package>
<package>
https://github.com/vimalkumarvelayudhan/riboseqr_wrapper_deps/raw/master/0.4.0/GenomicRanges_1.18.4.tar.gz?raw=true
</package>
<package>
https://github.com/vimalkumarvelayudhan/riboseqr_wrapper_deps/raw/master/0.4.0/abind_1.4-3.tar.gz?raw=true
</package>
<package>
https://github.com/vimalkumarvelayudhan/riboseqr_wrapper_deps/raw/master/0.4.0/baySeq_2.0.50.tar.gz?raw=true
</package>
<package>
https://github.com/vimalkumarvelayudhan/riboseqr_wrapper_deps/raw/master/0.4.0/riboSeqR_1.0.5.tar.gz?raw=true
</package>
</action>
</actions>
</install>
<readme>
Dependency installation for riboseqr_wrapper
</readme>
</package>
</tool_dependency>