annotate tool_dependencies.xml @ 0:085a17b297b1 draft default tip

planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/packages/package_python_3_4_pysam_0_8_3 commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa

<?xml version="1.0"?>
<tool_dependency>
    <package name="python" version="3.4">
      <repository changeset_revision="20ecf5cd3c0e" name="package_python_3_4" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
    </package>
    <package name="pysam" version="0.8.3">
        <install version="1.0">
            <actions>
                <action type="download_by_url">https://depot.galaxyproject.org/software/pysam/pysam_0.8.3_src_all.tar.gz</action>
                <action type="set_environment_for_install">
                    <repository changeset_revision="20ecf5cd3c0e" name="package_python_3_4" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
                        <package name="python" version="3.4" />
                    </repository>
                </action>
                <action type="make_directory">$INSTALL_DIR/lib/python</action>
                <action type="shell_command">
                    export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp;
                    python3 setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin
                </action>
                <action type="set_environment">
                    <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>
                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
                    <environment_variable action="set_to" name="PYTHONPATH_PYSAM">$INSTALL_DIR/lib/python</environment_variable>
                    <environment_variable action="set_to" name="PATH_PYSAM">$INSTALL_DIR/bin</environment_variable>
                    <environment_variable action="set_to" name="PYSAM_ROOT_DIR">$INSTALL_DIR</environment_variable>
                </action>
            </actions>
        </install>
        <readme>
            Installation of pysam, pyrex and python are required. The installation can be accessed via PYSAM_PATH.
        </readme>
    </package>
</tool_dependency>