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annotate tool_dependencies.xml @ 0:d71e21675123 draft

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planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/packages/package_python_3_4_bioext_0_17_3 commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
author nml
date Thu, 07 Jul 2016 09:57:47 -0400
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d71e21675123 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/packages/package_python_3_4_bioext_0_17_3 commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
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1 <?xml version="1.0"?>
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2 <tool_dependency>
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3 <package name="python" version="3.4">
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4 <repository changeset_revision="20ecf5cd3c0e" name="package_python_3_4" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
d71e21675123 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/packages/package_python_3_4_bioext_0_17_3 commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
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5 </package>
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6 <package name="pysam" version="0.8.3">
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7 <repository changeset_revision="085a17b297b1" name="package_python_3_4_pysam_0_8_3" owner="nml" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
d71e21675123 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/packages/package_python_3_4_bioext_0_17_3 commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
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8 </package>
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9 <package name="numpy" version="1.10.1">
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10 <repository changeset_revision="f182da2b1d78" name="package_python_3_4_numpy_1_10_1" owner="nml" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
d71e21675123 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/packages/package_python_3_4_bioext_0_17_3 commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
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11 </package>
d71e21675123 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/packages/package_python_3_4_bioext_0_17_3 commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
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12 <package name="biopython" version="1.66">
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13 <repository changeset_revision="cb43753d0467" name="package_python_3_4_biopython_1_66" owner="nml" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
d71e21675123 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/packages/package_python_3_4_bioext_0_17_3 commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
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14 </package>
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15 <package name="bioext" version="0.17.3">
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16 <install version="1.0">
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17 <actions>
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18 <action type="download_by_url">https://github.com/veg/BioExt/archive/0.17.3.tar.gz</action>
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19 <action type="set_environment_for_install">
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20 <repository changeset_revision="085a17b297b1" name="package_python_3_4_pysam_0_8_3" owner="nml" toolshed="https://toolshed.g2.bx.psu.edu">
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21 <package name="pysam" version="0.8.3" />
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22 </repository>
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23 <repository changeset_revision="f182da2b1d78" name="package_python_3_4_numpy_1_10_1" owner="nml" toolshed="https://toolshed.g2.bx.psu.edu">
d71e21675123 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/packages/package_python_3_4_bioext_0_17_3 commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
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24 <package name="numpy" version="1.10.1" />
d71e21675123 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/packages/package_python_3_4_bioext_0_17_3 commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
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25 </repository>
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26 <repository changeset_revision="cb43753d0467" name="package_python_3_4_biopython_1_66" owner="nml" toolshed="https://toolshed.g2.bx.psu.edu">
d71e21675123 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/packages/package_python_3_4_bioext_0_17_3 commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
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27 <package name="biopython" version="1.66" />
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28 </repository>
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29 <repository changeset_revision="20ecf5cd3c0e" name="package_python_3_4" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
d71e21675123 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/packages/package_python_3_4_bioext_0_17_3 commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
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30 <package name="python" version="3.4" />
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31 </repository>
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32 </action>
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33 <action type="make_directory">$INSTALL_DIR/lib/python</action>
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34 <action type="shell_command">
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35 export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp;
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36 export PATH=$PATH:$PATH_NUMPY &amp;&amp;
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37 export PYTHONPATH=$PYTHONPATH:$PYTHONPATH_NUMPY &amp;&amp;
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38 python3 setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin
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39 </action>
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40 <action type="set_environment">
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41 <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR</environment_variable>
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42 <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>
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43 <environment_variable action="append_to" name="PYTHONPATH">$ENV[PYTHONPATH_PYSAM]</environment_variable>
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44 <environment_variable action="append_to" name="PYTHONPATH">$ENV[PYTHONPATH_NUMPY]</environment_variable>
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45 <environment_variable action="append_to" name="PYTHONPATH">$ENV[PYTHONPATH_BIOPYTHON]</environment_variable>
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46 <environment_variable action="prepend_to" name="PATH">$ENV[PATH_NUMPY]</environment_variable>
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47 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
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48 <environment_variable action="set_to" name="PYTHONPATH_BIOEXT">$INSTALL_DIR/lib/python</environment_variable>
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49 <environment_variable action="set_to" name="PATH_BIOEXT">$INSTALL_DIR/bin</environment_variable>
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50 </action>
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51 </actions>
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52 </install>
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53 <readme>A few handy bioinformatics tools not already within BioPython</readme>
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54 </package>
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55 </tool_dependency>