Mercurial > repos > biopython > package_biopython_1_64
annotate tool_dependencies.xml @ 0:5477a05cc158 draft
Uploaded initial version based on Biopython 1.63 package
author | biopython |
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date | Mon, 02 Jun 2014 09:26:04 -0400 |
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children | b64c8edb7e45 |
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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="ef12a3a11d5b" name="package_numpy_1_7" owner="iuc" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" /> |
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5 </package> |
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6 <package name="biopython" version="1.64"> |
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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-1.64.tar.gz</action> |
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21 <action type="set_environment_for_install"> |
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22 <repository changeset_revision="ef12a3a11d5b" name="package_numpy_1_7" owner="iuc" toolshed="http://toolshed.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 <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> |