Mercurial > repos > iuc > package_rdkit_2013_03

annotate tool_dependencies.xml @ 5:55d51dcbd84e draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_rdkit_2013_03 commit 48fbe322d0f3ec023186989104ae4f4188b03a1d
author iuc
date Mon, 01 Jun 2015 22:43:19 -0400
parents dfc9c6a11322
children 34167468f87c
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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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a81880a37556 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_rdkit_2013_03 commit 45a64d82dfada34d826be98a1f7a0657f9148d59
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4 <repository changeset_revision="bbfe29f56566" name="package_numpy_1_7" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
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5 </package>
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6 <package name="boost" version="1.53.0">
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55d51dcbd84e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_rdkit_2013_03 commit 48fbe322d0f3ec023186989104ae4f4188b03a1d
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7 <repository changeset_revision="a3df665907d3" name="package_boost_1_53" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
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8 </package>
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9
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10 <package name="rdkit" version="2013_03_2">
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11 <install version="1.0">
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12 <actions>
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13 <!-- first action is always downloading -->
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14 <action type="download_by_url">http://rdkit.googlecode.com/files/RDKit_2013_03_2.tgz</action>
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15
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16 <!-- populate the environment variables from the dependend repos -->
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17 <action type="set_environment_for_install">
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a81880a37556 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_rdkit_2013_03 commit 45a64d82dfada34d826be98a1f7a0657f9148d59
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18 <repository changeset_revision="bbfe29f56566" name="package_numpy_1_7" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
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19 <package name="numpy" version="1.7.1" />
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20 </repository>
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55d51dcbd84e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_rdkit_2013_03 commit 48fbe322d0f3ec023186989104ae4f4188b03a1d
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21 <repository changeset_revision="a3df665907d3" name="package_boost_1_53" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
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22 <package name="boost" version="1.53.0" />
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23 </repository>
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24 </action>
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25
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26 <!-- PYTHONPATH_NUMPY is set in the numpy package -->
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27 <action type="shell_command">export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:`pwd`/lib/ &amp;&amp;
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28 export PYTHONPATH=$PYTHONPATH:`pwd`/ &amp;&amp;
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29 mkdir build &amp;&amp;
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30 cd build &amp;&amp;
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31 cmake .. -DBOOST_ROOT=$BOOST_ROOT_DIR -DCMAKE_INSTALL_PREFIX=$INSTALL_DIR/rdkit/ -DRDK_INSTALL_INTREE=OFF -DPYTHON_NUMPY_INCLUDE_PATH=$PYTHONPATH_NUMPY/numpy/core/include/</action>
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32 <action type="shell_command">cd ./build &amp;&amp; make </action>
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33 <action type="shell_command">cd ./build &amp;&amp; make install</action>
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34
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35 <action type="set_environment">
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36 <environment_variable action="set_to" name="RDBASE">$INSTALL_DIR/rdkit</environment_variable>
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37 <environment_variable action="append_to" name="LD_LIBRARY_PATH">$INSTALL_DIR/rdkit/lib/</environment_variable>
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38 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/rdkit/bin</environment_variable>
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39 <!-- on fedora everything is installed under lib64 -->
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40 <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR/rdkit/lib/python2.7/site-packages/</environment_variable>
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41 <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR/rdkit/lib64/python2.7/site-packages/</environment_variable>
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42 <environment_variable action="prepend_to" name="PYTHONPATH">$ENV[PYTHONPATH_NUMPY]</environment_variable>
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43 <environment_variable action="append_to" name="LD_LIBRARY_PATH">$ENV[BOOST_ROOT_DIR]/lib/</environment_variable>
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44 </action>
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45 </actions>
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46 </install>
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47 <readme>Compiling rdkit requires cmake, python headers, sqlite3, flex and bison.</readme>
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48 </package>
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49 </tool_dependency>