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view tool_dependencies.xml @ 15:a08df50089e2

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ChemicalToolBoX update.
author Bjoern Gruening <bjoern.gruening@gmail.com>
date Tue, 23 Jul 2013 00:51:20 +0200
parents 2560d8a02782
children 4663c03127f7
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<?xml version='1.0' encoding='utf-8'?>
<tool_dependency>
    <package name="numpy" version="1.7.1">
        <repository changeset_revision="a0f0a86440ca" name="package_numpy_1_7" owner="bgruening" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
    </package>
    <package name="boost" version="1.53.0">
        <repository changeset_revision="f5b13e56a321" name="package_boost_1_53" owner="bgruening" prior_installation_required="True" toolshed="http://testtoolshed.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="a0f0a86440ca" name="package_numpy_1_7" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu/">
                        <package name="numpy" version="1.7.1" />
                    </repository>
                    <repository changeset_revision="f5b13e56a321" name="package_boost_1_53" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu/">
                        <package name="boost" version="1.53.0" />
                    </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">$INSTALL_DIR/rdkit/bin</environment_variable>
                    <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR/rdkit/lib/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>