Mercurial > repos > ulfschaefer > package_python_2_7_biopython_1_66
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author | ulfschaefer |
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date | Wed, 16 Dec 2015 07:19:14 -0500 |
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<?xml version="1.0"?> <tool_dependency> <package name="python" version="2.7.10"> <repository changeset_revision="0339c4a9b87b" name="package_python_2_7_10" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> <package name="numpy" version="1.9"> <repository changeset_revision="794f5cf3bb5d" name="package_python_2_7_numpy_1_9" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> <package name="biopython" version="1.66"> <readme> This package is a modified version of the package package_biopython_1_66 owned by 'biopython' (copyright Peter Cock) revision 8433ee4531ff. Dependencies of this package have been modified to provide Biopython for Python 2.7.10. 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-1.66.tar.gz</action> <action type="set_environment_for_install"> <repository changeset_revision="794f5cf3bb5d" name="package_python_2_7_numpy_1_9" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"> <package name="numpy" version="1.9" /> </repository> </action> <action type="make_directory">$INSTALL_DIR/lib/python</action> <action type="shell_command"> export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python && export PATH=$PATH:$PATH_NUMPY && export PYTHONPATH=$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="set_to" name="PYTHONPATH_BIOPYTHON">$INSTALL_DIR/lib/python</environment_variable> </action> </actions> </install> </package> </tool_dependency>