<?xml version="1.0"?>
<tool_dependency>
    <package name="numpy" version="1.6.2">
        <install version="1.0">
            <actions>
                <action type="download_by_url">http://pypi.python.org/packages/source/n/numpy/numpy-1.6.2.tar.gz</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 --home $INSTALL_DIR --install-scripts $INSTALL_DIR/bin</action>
                <action type="set_environment">
                    <environment_variable name="PYTHONPATH" action="append_to">$INSTALL_DIR/lib/python</environment_variable>
                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
                </action>
            </actions>
        </install>
        <readme>
        </readme>
    </package>

    <package name="htseq" version="0.5.4p1">
        <install version="1.0">
            <actions>
                <action type="download_by_url">https://pypi.python.org/packages/source/H/HTSeq/HTSeq-0.5.4p1.tar.gz</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 $INSTALL_DIR/bin</action>
                <action type="set_environment">
                    <environment_variable name="PYTHONPATH" action="append_to">$INSTALL_DIR/lib/python:$INSTALL_DIR/lib64/python</environment_variable>
                    <environment_variable name="PATH" action="prepend_to">$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>

    <package name="samtools" version="0.1.18">
        <install version="1.0">
            <actions>
                <action type="download_by_url">http://sourceforge.net/projects/samtools/files/samtools/0.1.18/samtools-0.1.18.tar.bz2</action>
                <action type="shell_command">sed -i.bak -e 's/-lcurses/-lncurses/g' Makefile</action>
                <action type="shell_command">make</action>
                <action type="move_file">
                    <source>samtools</source>
                    <destination>$INSTALL_DIR/bin</destination>
                </action>
                <action type="move_file">
                    <source>misc/maq2sam-long</source>
                    <destination>$INSTALL_DIR/bin</destination>
                </action>
                <action type="set_environment">
                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
                </action>
            </actions>
        </install>
        <readme>
            Compiling SAMtools requires the ncurses and zlib development libraries.
        </readme>
    </package>

    <package name="picard" version="1.56.0">
        <install version="1.0">
            <actions>
                <action type="download_by_url">http://downloads.sourceforge.net/project/picard/picard-tools/1.56/picard-tools-1.56.zip</action>
                <action type="move_directory_files">
                    <source_directory>picard-tools-1.56</source_directory>
                    <destination_directory>$INSTALL_DIR/jars</destination_directory>
                </action>
                <action type="set_environment">
                    <environment_variable name="JAVA_JAR_PATH" action="set_to">$INSTALL_DIR/jars</environment_variable>
                </action>
            </actions>
        </install>
        <readme>
        </readme>
    </package>
</tool_dependency>