annotate tool_dependencies.xml @ 2:ae369c08a2a7 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_openbabel_2_3 commit 2e18fe350712147421228210013814bc0aeec120

<?xml version="1.0"?>
<tool_dependency>
    <package name="eigen3" version="3.1.3">
        <repository changeset_revision="baedf7f82cc3" name="package_eigen_3_1" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
    </package>
    <package name="openbabel" version="2.3.2">
        <install version="1.0">
            <actions>
                <action sha256sum="4eaca26679aa6cc85ebf96af19191472ac63ca442c36b0427b369c3a25705188" type="download_by_url">https://depot.galaxyproject.org/software/openbabel/openbabel_2.3.2_src_all.tar.gz</action>
                <action type="set_environment_for_install">
                    <repository changeset_revision="baedf7f82cc3" name="package_eigen_3_1" owner="iuc" toolshed="https://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="make_install" />
                <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>