<?xml version="1.0"?>
<tool_dependency>

    <package name="numpy" version="1.7.1">
        <repository changeset_revision="028df1ddd7a2" name="package_numpy_1_7" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" />
    </package>

    <package name="samtools" version="0.1.19">
        <repository changeset_revision="00e17a794a2e" name="package_samtools_0_1_19" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" />
    </package>

    <package name="picard" version="1.56.0">
        <repository changeset_revision="61e41d21cb6f" name="package_picard_1_56_0" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" />
    </package>

    <package name="htseq" version="0.5.4p5">
        <install version="1.0">
            <actions>
                <action type="download_by_url">https://pypi.python.org/packages/source/H/HTSeq/HTSeq-0.5.4p5.tar.gz</action>
                <!-- populate the environment variables from the dependend repos -->
                <action type="set_environment_for_install">
                    <repository changeset_revision="028df1ddd7a2" name="package_numpy_1_7" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu">
                        <package name="numpy" version="1.7.1" />
                   </repository>
                </action>
                <action type="make_directory">$INSTALL_DIR/lib/python</action> <!-- Not sure why these must be made apriori, but install fails otherwise -->
                <action type="make_directory">$INSTALL_DIR/lib64/python</action> <!-- Not sure why these must be made apriori, but install fails otherwise -->
                <action type="shell_command">export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python:$INSTALL_DIR/lib64/python &amp;&amp; python setup.py install --home $INSTALL_DIR --install-scripts $INSTALL_DIR/bin</action>
                <action type="set_environment">
                    <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR/lib/python:$INSTALL_DIR/lib64/python</environment_variable>
                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
                </action>
            </actions>
        </install>
        <readme>
            Installation of HTSeq requires Python 2.5+ (does not yet work with Python 3), and the Nympy Python package.
        </readme>
    </package>

</tool_dependency>