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<?xml version="1.0"?>
<tool_dependency>
    <package name="samtools" version="0.1.19">
        <repository changeset_revision="96aab723499f" name="package_samtools_0_1_19" owner="iuc" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" />
    </package>
    <package name="sparsehash" version="2.0.2">
        <repository changeset_revision="2cc9627ae29c" name="package_sparsehash_2_0_2" owner="iuc" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" />
    </package>
    <package name="stacks" version="1.32">
        <install version="1.0">
            <actions>
                <!-- first action is always downloading -->
                <action type="download_by_url">http://catchenlab.life.illinois.edu/stacks/source/stacks-1.32.tar.gz</action>

                <!-- populate the environment variables from the dependend repos -->
                <action type="set_environment_for_install">
                    <repository changeset_revision="96aab723499f" name="package_samtools_0_1_19" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu">
                        <package name="samtools" version="0.1.19" />
                    </repository>
                    <repository changeset_revision="2cc9627ae29c" name="package_sparsehash_2_0_2" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu">
                        <package name="sparsehash" version="2.0.2" />
                    </repository>
                </action>

                <action type="autoconf">--enable-sparsehash --enable-bam --with-bam-include-path=${BAM_ROOT}/include --with-bam-lib-path=${BAM_LIB_PATH}</action>

                <action type="set_environment">
                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
                </action>
            </actions>
        </install>
    </package>
</tool_dependency>