<?xml version="1.0"?>
<package name="samtools" version="0.1.18">
    <repository toolshed="http://testtoolshed.g2.bx.psu.edu/" name="package_samtools_0_1_18" owner="devteam " changeset_revision="a7936f4ea405" />
</package>
<tool_dependency>
    <set_environment version="1.0">
        <environment_variable name="SCRIPT_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable>
    </set_environment>
    <package name="bowtie2" version="2.1.0">
        <install version="1.0">
            <actions>
                <action type="download_by_url">http://downloads.sourceforge.net/project/bowtie-bio/bowtie2/2.1.0/bowtie2-2.1.0-source.zip</action>
                <action type="shell_command">make</action>
                <action type="move_file">
                    <source>bowtie2</source>
                    <destination>$INSTALL_DIR/bin</destination>
                </action>
                <action type="move_file">
                    <source>bowtie2-align</source>
                    <destination>$INSTALL_DIR/bin</destination>
                </action>
                <action type="move_file">
                    <source>bowtie2-build</source>
                    <destination>$INSTALL_DIR/bin</destination>
                </action>
                <action type="shell_command">chmod +x $INSTALL_DIR/bin/bowtie2</action>
                <action type="set_environment">
                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
                </action>
            </actions>
        </install>
        <readme>
Compiling bowtie2 requires zlib and libpthread to be present on your system.
        </readme>
    </package>
    <package name="bowtie" version="0.12.8">
        <install version="1.0">
            <actions>
                <action type="download_by_url">http://downloads.sourceforge.net/project/bowtie-bio/bowtie/0.12.8/bowtie-0.12.8-src.zip</action>
                <action type="shell_command">make</action>
                <action type="move_file">
                    <source>bowtie</source>
                    <destination>$INSTALL_DIR/bin</destination>
                </action>
                <action type="move_file">
                    <source>bowtie-inspect</source>
                    <destination>$INSTALL_DIR/bin</destination>
                </action>
                <action type="move_file">
                    <source>bowtie-build</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>
        </readme>
    </package>
</tool_dependency>