annotate tool_dependencies.xml @ 7:e6f49ee3509c draft

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<?xml version="1.0"?>
<tool_dependency>
    <package name="samtools" version="0.1.19">
        <repository changeset_revision="279806044d60" name="package_samtools_0_1_19" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
    </package>
    <package name="R_3_0_1" version="3.0.1">
        <repository changeset_revision="c5ff6dd33c79" name="package_r_3_0_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
    </package>
    <package name="eden" version="1.1">
        <repository changeset_revision="8087eef83c35" name="package_eden_1_1" owner="rnateam" toolshed="https://toolshed.g2.bx.psu.edu" />
    </package>
    <package name="mcl" version="12.135">
        <repository changeset_revision="9f59d1a59999" name="package_mcl_12_135" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
    </package>
    <package name="blockclust_rlibs" version="1.0">
         <install version="1.0">
            <actions>
                <action type="setup_r_environment">
                    <repository changeset_revision="c5ff6dd33c79" name="package_r_3_0_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
                        <package name="R_3_0_1" version="3.0.1" />
                    </repository>
                    <package>https://github.com/bgruening/download_store/raw/master/blockclust/r-packages/ape_3.0-11.tar.gz</package>
                    <package>https://github.com/bgruening/download_store/raw/master/blockclust/r-packages/plyr_1.8.tar.gz</package>
                    <package>https://github.com/bgruening/download_store/raw/master/blockclust/r-packages/digest_0.6.4.tar.gz</package>
                    <package>https://github.com/bgruening/download_store/raw/master/blockclust/r-packages/gtable_0.1.2.tar.gz</package>
                    <package>https://github.com/bgruening/download_store/raw/master/blockclust/r-packages/dichromat_2.0-0.tar.gz</package>
                    <package>https://github.com/bgruening/download_store/raw/master/blockclust/r-packages/colorspace_1.2-4.tar.gz</package>
                    <package>https://github.com/bgruening/download_store/raw/master/blockclust/r-packages/munsell_0.4.2.tar.gz</package>
                    <package>https://github.com/bgruening/download_store/raw/master/blockclust/r-packages/labeling_0.2.tar.gz</package>
                    <package>https://github.com/bgruening/download_store/raw/master/blockclust/r-packages/RColorBrewer_1.0-5.tar.gz</package>
                    <package>https://github.com/bgruening/download_store/raw/master/blockclust/r-packages/stringr_0.6.2.tar.gz</package>
                    <package>https://github.com/bgruening/download_store/raw/master/blockclust/r-packages/scales_0.2.3.tar.gz</package>
                    <package>https://github.com/bgruening/download_store/raw/master/blockclust/r-packages/proto_0.3-10.tar.gz</package>
                    <package>https://github.com/bgruening/download_store/raw/master/blockclust/r-packages/reshape2_1.2.2.tar.gz</package>
                    <package>https://github.com/bgruening/download_store/raw/master/blockclust/r-packages/ggplot2_0.9.3.1.tar.gz</package>
                    <package>https://github.com/bgruening/download_store/raw/master/blockclust/r-packages/squash_1.0.1.tar.gz</package>
                </action>
            </actions>
        </install>
        <readme>

        </readme>
    </package>
    <package name="blockclust" version="1.0">
        <install version="1.0">
            <actions>
                <action type="download_by_url">https://github.com/bgruening/download_store/raw/master/blockclust/blockclust-1.0.tar.gz</action>
                <action type="shell_command">make</action>
                <action type="move_file">
                    <source>BlockClust</source>
                    <destination>$INSTALL_DIR/bin</destination>
                </action>
                <action type="move_file">
                    <source>BlockClustPipeLine.pl</source>
                    <destination>$INSTALL_DIR/bin</destination>
                </action>
                <action type="move_file">
                    <source>perf</source>
                    <destination>$INSTALL_DIR/bin</destination>
                </action>
                <action type="move_file">
                    <source>plotClusters.R</source>
                    <destination>$INSTALL_DIR/bin</destination>
                </action>
                <action type="move_file">
                    <source>blockclust.config</source>
                    <destination>$INSTALL_DIR/data/</destination>
                </action>
                <action type="move_file">
                    <source>rfam_map.txt</source>
                    <destination>$INSTALL_DIR/data/</destination>
                </action>
                <action type="make_directory">$INSTALL_DIR/data/annotations</action>
                <action type="download_file">https://github.com/bgruening/download_store/raw/master/blockclust/blockclust-data-1.0/annotations/dm3.tar.gz</action>
                <action type="shell_command">tar xfvz dm3.tar.gz -C $INSTALL_DIR/data/annotations/</action>
                <action type="download_file">https://github.com/bgruening/download_store/raw/master/blockclust/blockclust-data-1.0/annotations/hg19.tar.gz</action>
                <action type="shell_command">tar xfvz hg19.tar.gz -C $INSTALL_DIR/data/annotations/</action>
                <action type="download_file">https://github.com/bgruening/download_store/raw/master/blockclust/blockclust-data-1.0/annotations/mm10.tar.gz</action>
                <action type="shell_command">tar xfvz mm10.tar.gz -C $INSTALL_DIR/data/annotations/</action>
                <action type="download_file">https://github.com/bgruening/download_store/raw/master/blockclust/blockclust-data-1.0/annotations/panTro4.tar.gz</action>
                <action type="shell_command">tar xfvz panTro4.tar.gz -C $INSTALL_DIR/data/annotations/</action>
                <action type="download_file">https://github.com/bgruening/download_store/raw/master/blockclust/blockclust-data-1.0/annotations/rheMac3.tar.gz</action>
                <action type="shell_command">tar xfvz rheMac3.tar.gz -C $INSTALL_DIR/data/annotations/</action>
                <action type="download_file">https://github.com/bgruening/download_store/raw/master/blockclust/blockclust-data-1.0/annotations/celWS235.tar.gz</action>
                <action type="shell_command">tar xfvz celWS235.tar.gz -C $INSTALL_DIR/data/annotations/</action>
                <action type="download_file">https://github.com/bgruening/download_store/raw/master/blockclust/blockclust-data-1.0/annotations/tair10.tar.gz</action>
                <action type="shell_command">tar xfvz tair10.tar.gz -C $INSTALL_DIR/data/annotations/</action>
                <action type="download_file">https://github.com/bgruening/download_store/raw/master/blockclust/blockclust-data-1.0/models.tar.gz</action>
                <action type="shell_command">tar xfvz models.tar.gz -C $INSTALL_DIR/data/</action>
                <action type="set_environment">
                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
                    <environment_variable action="set_to" name="BLOCKCLUST_DATA_PATH">$INSTALL_DIR/data</environment_variable>
                </action>
            </actions>
        </install>
        <readme>
	
        </readme>
    </package>
</tool_dependency>