view tool_dependencies.xml @ 18:cff63cf0dea8

Update tool_dependencies to install package from pip

<?xml version="1.0"?>
<tool_dependency>
    <package name="ez_setup" version="0.9">
        <repository changeset_revision="f50b27b88d30" name="package_ez_setup_0_9" owner="iuc"
            prior_installation_required="True"/>
    </package>
    <package name="riboplot" version="0.1.0">
        <install version="1.0">
            <actions>
                <action type="download_by_url">https://pypi.python.org/packages/source/r/riboplot/riboplot-0.1.0.tar.gz</action>
                <action type="set_environment_for_install">
                    <repository changeset_revision="f50b27b88d30" name="package_ez_setup_0_9" owner="iuc">
                        <package name="ez_setup" version="0.9" />
                    </repository>
                </action>
                <action type="make_directory">$INSTALL_DIR/lib/python</action>
                <action type="shell_command">export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp; python 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">$INSTALL_DIR/bin</environment_variable>
                    <environment_variable action="set_to" name="RIBOPLOT_PATH">$INSTALL_DIR</environment_variable>
                </action>
            </actions>
        </install>
        <readme>
           Requires installation of matplotlib 1.3.1 and pysam 0.8.3. RNA coverage requires bedtools installed.
        </readme>
    </package>
</tool_dependency>