annotate tool_dependencies.xml @ 2:842dd2fa4ace draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_rdkit_2012_12 commit 710c0d73202078bd43efd595c28526ba26c8fa50-dirty

<?xml version="1.0"?>
<tool_dependency>
    <package name="numpy" version="1.7.1">
        <repository changeset_revision="300877695495" name="package_numpy_1_7" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
    </package>
    <package name="boost" version="1.55.0">
        <repository changeset_revision="f0da948c5302" name="package_boost_1_55" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
    </package>

    <package name="rdkit" version="2012_12_1">
        <install version="1.0">
            <actions>
                <!-- first action is always downloading -->
                <action type="download_by_url">http://downloads.sourceforge.net/project/rdkit/rdkit/Q4_2012/RDKit_2012_12_1.tgz</action>

                <!-- populate the environment variables from the dependend repos -->
                <action type="set_environment_for_install">
                    <repository changeset_revision="300877695495" name="package_numpy_1_7" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
                        <package name="numpy" version="1.7.1" />
                    </repository>
                    <repository changeset_revision="f0da948c5302" name="package_boost_1_55" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
                        <package name="boost" version="1.55.0" />
                    </repository>
                </action>

                <!-- PYTHONPATH_NUMPY is set in the numpy package -->
                <action type="shell_command">export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:`pwd`/lib/ &amp;&amp;
                    export PYTHONPATH=$PYTHONPATH:`pwd`/ &amp;&amp;
                    mkdir build &amp;&amp;
                    cd build &amp;&amp;
                    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>
                <action type="shell_command">cd ./build &amp;&amp; make </action>
                <action type="shell_command">cd ./build &amp;&amp; make install</action>

                <action type="set_environment">
                    <environment_variable action="set_to" name="RDBASE">$INSTALL_DIR/rdkit</environment_variable>
                    <environment_variable action="append_to" name="LD_LIBRARY_PATH">$INSTALL_DIR/rdkit/lib/</environment_variable>
                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/rdkit/bin</environment_variable>
                    <!-- on fedora everything is installed under lib64 -->
                    <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR/rdkit/lib/python2.7/site-packages/</environment_variable>
                    <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR/rdkit/lib64/python2.7/site-packages/</environment_variable>
                    <environment_variable action="prepend_to" name="PYTHONPATH">$ENV[PYTHONPATH_NUMPY]</environment_variable>
                    <environment_variable action="append_to" name="LD_LIBRARY_PATH">$ENV[BOOST_ROOT_DIR]/lib/</environment_variable>
                </action>
            </actions>
        </install>
        <readme>Compiling rdkit requires cmake, python headers, sqlite3, flex and bison.</readme>
    </package>
</tool_dependency>