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1 <?xml version="1.0"?>
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2 <tool_dependency>
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3 <package name="numpy" version="1.7.1">
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4 <repository changeset_revision="793c48909d53" name="package_numpy_1_7" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
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5 </package>
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6 <package name="biopython" version="1.61">
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7 <install version="1.0">
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8 <actions>
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9 <action type="download_by_url">https://pypi.python.org/packages/source/b/biopython/biopython-1.61.tar.gz</action>
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10 <action type="set_environment_for_install">
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11 <repository changeset_revision="793c48909d53" name="package_numpy_1_7" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
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12 <package name="numpy" version="1.7.1" />
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13 </repository>
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14 </action>
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15 <action type="make_directory">$INSTALL_DIR/lib/python</action>
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16 <action type="shell_command">
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17 export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &&
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18 export PATH=$PATH:$PATH_NUMPY &&
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19 export PYTHONPATH=$PYTHONPATH:$PYTHONPATH_NUMPY:$PYTHONPATH_MATPLOTLIB &&
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20 python setup.py install --install-lib $INSTALL_DIR/lib/python
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21 </action>
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22 <action type="set_environment">
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23 <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>
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24
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25 <environment_variable action="append_to" name="PYTHONPATH">$ENV[PYTHONPATH_NUMPY]</environment_variable>
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26 <environment_variable action="prepend_to" name="PATH">$ENV[PATH_NUMPY]</environment_variable>
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27 <environment_variable action="append_to" name="PYTHONPATH">$ENV[PYTHONPATH_MATPLOTLIB]</environment_variable>
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28
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29 <environment_variable action="set_to" name="PYTHONPATH_BIOPYTHON">$INSTALL_DIR/lib/python</environment_variable>
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30 </action>
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31 </actions>
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32 </install>
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33 <readme>The PYTHONPATH for biopython can be accessed through PYTHONPATH_BIOPYTHON.</readme>
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34 </package>
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35 </tool_dependency>
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