annotate tool_dependencies.xml @ 1:e5ef70185d24 draft

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<?xml version="1.0"?>
<tool_dependency>
    <package name="eigen3" version="3.1.3">
        <repository changeset_revision="b8ed0e76f501" name="package_eigen_3_1" owner="iuc" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" />
    </package>
    <package name="openbabel" version="2.3.2">
        <install version="1.0">
            <actions>
                <action type="download_by_url">http://downloads.sourceforge.net/project/openbabel/openbabel/2.3.2/openbabel-2.3.2.tar.gz</action>

                <!-- populate the environment variables from the dependend repos -->
                <action type="set_environment_for_install">
                    <repository changeset_revision="b8ed0e76f501" name="package_eigen_3_1" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu">
                        <package name="eigen3" version="3.1.3" />
                    </repository>
                </action>

                <!--
                    Huge hack, to point to the actual python lib path. Cmake gets confused with mixed python versions (2.x and 3.x) and we need to point explicitely to the recent version.
                -->
                <action type="shell_command">cmake . -DPYTHON_BINDINGS=ON -DCMAKE_INSTALL_PREFIX=$INSTALL_DIR -DEIGEN3_INCLUDE_DIR=$EIGEN3_SOURCE_PATH -DPYTHON_LIBRARY=`python -c 'import distutils.sysconfig; print "%s/libpython%s.so" % (distutils.sysconfig.get_config_var("LIBPL"), distutils.sysconfig.get_python_version())'`</action>
                <action type="shell_command">make</action>
                <action type="shell_command">make install</action>
                <action type="set_environment">
                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
                    <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR/lib</environment_variable>
                    <!-- internal variables for open babel -->
                    <environment_variable action="set_to" name="BABEL_DATADIR">$INSTALL_DIR/share/openbabel</environment_variable>
                    <environment_variable action="set_to" name="BABEL_LIBDIR">$INSTALL_DIR/lib/openbabel/2.3.2</environment_variable>
                    <!-- galaxy variables for other tool wrappers -->
                    <environment_variable action="set_to" name="OPENBABEL_LIB_DIR">$INSTALL_DIR/lib</environment_variable>
                    <environment_variable action="set_to" name="OPENBABEL_INCLUDE_DIR">$INSTALL_DIR/include</environment_variable>
                    <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$INSTALL_DIR/lib/</environment_variable>
                    <environment_variable action="prepend_to" name="CPLUS_INCLUDE_PATH">$INSTALL_DIR/include</environment_variable>
                    <environment_variable action="prepend_to" name="C_INCLUDE_PATH">$INSTALL_DIR/include</environment_variable>
                </action>
            </actions>
        </install>
        <readme>Compiling OpenBabel requires g++ and CMake 2.4+. Optional but required for a few features are the cairo development libraries. OPENBABEL_INCLUDE_DIR and OPENBABEL_LIB_DIR can be accessed from other tool wrappers.</readme>
    </package>
</tool_dependency>