| Previous changeset 2:b482933a6de5 (2013-08-12) Next changeset 4:689e9fb41527 (2015-10-22) |
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Commit message:
Removed trace of MatPlotLib |
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modified:
tool_dependencies.xml |
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| diff -r b482933a6de5 -r ae9dda584395 tool_dependencies.xml --- a/tool_dependencies.xml Mon Aug 12 11:29:41 2013 -0400 +++ b/tool_dependencies.xml Tue Sep 17 04:54:28 2013 -0400 |
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| @@ -4,6 +4,17 @@ <repository changeset_revision="74c21f9bdc39" name="package_numpy_1_7" owner="iuc" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" /> </package> <package name="biopython" version="1.61"> + <readme> +This Galaxy Tool Shed package installs Biopython from source, having +first installed NumPy which is a build time depencency. This requires +and assumes a standard C compiler is already installed, along with +the Python header files. + +Development of this dependency definition is being done here on GitHub: +https://github.com/biopython/galaxy_packages + +The PYTHONPATH for biopython can be accessed through PYTHONPATH_BIOPYTHON. + </readme> <install version="1.0"> <actions> <action type="download_by_url">https://pypi.python.org/packages/source/b/biopython/biopython-1.61.tar.gz</action> @@ -16,20 +27,16 @@ <action type="shell_command"> export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python && export PATH=$PATH:$PATH_NUMPY && - export PYTHONPATH=$PYTHONPATH:$PYTHONPATH_NUMPY:$PYTHONPATH_MATPLOTLIB && + export PYTHONPATH=$PYTHONPATH:$PYTHONPATH_NUMPY && python setup.py 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="PYTHONPATH">$ENV[PYTHONPATH_NUMPY]</environment_variable> <environment_variable action="prepend_to" name="PATH">$ENV[PATH_NUMPY]</environment_variable> - <environment_variable action="append_to" name="PYTHONPATH">$ENV[PYTHONPATH_MATPLOTLIB]</environment_variable> - <environment_variable action="set_to" name="PYTHONPATH_BIOPYTHON">$INSTALL_DIR/lib/python</environment_variable> - </action> + </action> </actions> </install> - <readme>The PYTHONPATH for biopython can be accessed through PYTHONPATH_BIOPYTHON.</readme> </package> </tool_dependency> |