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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="1.9">
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4 <repository changeset_revision="9cc1138e5e3e" name="package_numpy_1_9" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
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5 </package>
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6 <package name="biopython" version="1.65">
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7 <readme>
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8 This Galaxy Tool Shed package installs Biopython from source, having
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9 first installed NumPy which is a build time depencency. This requires
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10 and assumes a standard C compiler is already installed, along with
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11 the Python header files.
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12
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13 Development of this dependency definition is being done here on GitHub:
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14 https://github.com/biopython/galaxy_packages
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15
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16 The PYTHONPATH for biopython can be accessed through PYTHONPATH_BIOPYTHON.
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17 </readme>
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18 <install version="1.0">
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19 <actions>
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20 <action type="download_by_url">https://pypi.python.org/packages/source/b/biopython/biopython-1.65.tar.gz</action>
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21 <action type="set_environment_for_install">
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22 <repository changeset_revision="9cc1138e5e3e" name="package_numpy_1_9" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
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23 <package name="numpy" version="1.9" />
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24 </repository>
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25 </action>
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26 <action type="make_directory">$INSTALL_DIR/lib/python</action>
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27 <action type="shell_command">
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28 export PYTHONPATH=$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 &&
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31 python setup.py install --install-lib $INSTALL_DIR/lib/python
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32 </action>
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33 <action type="set_environment">
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34 <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>
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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="set_to" name="PYTHONPATH_BIOPYTHON">$INSTALL_DIR/lib/python</environment_variable>
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38 </action>
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39 </actions>
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40 </install>
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41 </package>
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42 </tool_dependency>
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