view tool_dependencies.xml @ 3:898c17f918c7 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_sailfish_0_6 commit e8e971905f5fce11a99d51b1399af45288389d76

<?xml version="1.0"?>
<tool_dependency>
    <package name="boost" version="1.53.0">
        <repository changeset_revision="2c9b2a72c9d7" name="package_boost_1_53" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
    </package>

    <package name="sailfish" version="0.6.3">
        <install version="1.0">
            <actions>
                <!-- first action is always downloading -->
                <action type="download_by_url">https://github.com/kingsfordgroup/sailfish/archive/v0.6.3.tar.gz</action>

                <!-- populate the environment variables from the dependend repos -->
                <action type="set_environment_for_install">
                    <repository changeset_revision="2c9b2a72c9d7" name="package_boost_1_53" owner="iuc" toolshed="https://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">
                    mkdir build &amp;&amp;
                    cd build &amp;&amp;
                    cmake .. -DBOOST_ROOT=$BOOST_ROOT_DIR -DCMAKE_INSTALL_PREFIX=$INSTALL_DIR</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="append_to" name="LD_LIBRARY_PATH">$INSTALL_DIR/lib/</environment_variable>
                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
                    <environment_variable action="append_to" name="LD_LIBRARY_PATH">$ENV[BOOST_ROOT_DIR]/lib/</environment_variable>
                </action>
            </actions>
        </install>
        <readme>Compiling sailfish requires cmake and C++11 compiler (usually gcc).</readme>
    </package>
</tool_dependency>