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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="ad6ebe2c75ef" name="package_numpy_1_7" owner="bgruening" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
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5 </package>
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6 <package name="matplotlib" version="1.2.1">
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7 <repository changeset_revision="c888aa8ed318" name="package_matplotlib_1_2" owner="bgruening" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
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8 </package>
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9 <!-- TODO reportlab -> Python Imaging Library
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10 <package name="reportlab" version="1.2.1">
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11 <repository name="package_reportlab_1_2" owner="bgruening" prior_installation_required="True" />
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12 </package>
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13 -->
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14 <package name="biopython" version="1.61">
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15 <install version="1.0">
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16 <actions>
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17 <action type="download_by_url">https://pypi.python.org/packages/source/b/biopython/biopython-1.61.tar.gz</action>
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18 <action type="set_environment_for_install">
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19 <repository changeset_revision="c888aa8ed318" name="package_matplotlib_1_2" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu">
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20 <package name="matplotlib" version="1.2.1" />
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21 </repository>
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22 <repository changeset_revision="ad6ebe2c75ef" name="package_numpy_1_7" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu">
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23 <package name="numpy" version="1.7.1" />
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24 </repository>
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25 </action>
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26
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27 <action type="make_directory">$INSTALL_DIR/lib/python</action>
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28 <action type="shell_command">export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &&
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29 export PATH=$PATH:$PATH_NUMPY &&
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30 export PYTHONPATH=$PYTHONPATH:$PYTHONPATH_NUMPY:$PYTHONPATH_MATPLOTLIB &&
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31 python setup.py install --home $INSTALL_DIR</action>
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32 <action type="set_environment">
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33 <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>
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34
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35 <environment_variable action="append_to" name="PYTHONPATH">$ENV[PYTHONPATH_NUMPY]</environment_variable>
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36 <environment_variable action="prepend_to" name="PATH">$ENV[PATH_NUMPY]</environment_variable>
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37 <environment_variable action="append_to" name="PYTHONPATH">$ENV[PYTHONPATH_MATPLOTLIB]</environment_variable>
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38
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39 <environment_variable action="set_to" name="PYTHONPATH_BIOPYTHON">$INSTALL_DIR/lib/python</environment_variable>
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40
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41 </action>
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42 </actions>
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43 </install>
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44 <readme>The PYTHONPATH for scipy can be accessed through PYTHONPATH_BIOPYTHON.</readme>
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45 </package>
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46 </tool_dependency>
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