view tool_dependencies.xml @ 53:44059c9e7c02 draft

planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit adc1ac50269e02570e7ce12c732637bdd3f9a547-dirty

<?xml version="1.0"?>
<tool_dependency>
    <!-- UCSC Tools in  -->
    <!-- Useful for HAC are:
        - twoBitInfo
        - sort
        - bedToBigBed
        - gff3ToGenePred
        - gtfToGenePred
        - genePredToBed
        - genePredToBigGenePred
        - faToTwoBit
        - samtools
        - pslToBigPsl
    -->
    <package name="samtools" version="1.2">
        <repository changeset_revision="5b7172f9b230" name="package_samtools_1_2" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
    </package>

    <package name="ucsc_tools_340" version="1.0">
        <install version="1.0">
            <actions_group>
                <actions architecture="x86_64" os="linux">
                    <action type="download_by_url">http://old-gep.wustl.edu/~galaxy/ucsc_tools_340.tar.gz</action>
                    <action type="move_directory_files">
                        <source_directory>.</source_directory>
                        <destination_directory>$INSTALL_DIR/bin</destination_directory>
                    </action>
                </actions>
                <action type="set_environment">
                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
                </action>
            </actions_group>
         </install>
         <readme>The well known UCSC tools from Jim Kent.</readme>
    </package>

    <!-- package ucsc_bigwig is created by Wilson Leung -->
    <package name="ucsc_bigwig" version="340">
        <install version="1.0">
            <actions_group>
                <actions architecture="x86_64" os="darwin">
                    <action sha256sum="a34c57a9fb3c36a984b8fa879a99697c994cd981a1277663d372638e4dec8bb2" type="download_by_url">
                        http://old-gep.wustl.edu/~wilson/packages/ucsc_bigwig/ucsc_bigwig_340_macOS_x86_64.tar.gz
                    </action>
                    <action type="move_directory_files">
                        <source_directory>bin</source_directory>
                        <destination_directory>$INSTALL_DIR/bin</destination_directory>
                    </action>
                </actions>

                <actions architecture="x86_64" os="linux">
                    <action sha256sum="0d2bd886e312980e0ae58ae912315beeeac612fd1783c959b4eabd62cffd8512" type="download_by_url">
                        http://old-gep.wustl.edu/~wilson/packages/ucsc_bigwig/ucsc_bigwig_340_linux_x86_64.tar.gz
                    </action>
                    <action type="move_directory_files">
                        <source_directory>bin</source_directory>
                        <destination_directory>$INSTALL_DIR/bin</destination_directory>
                    </action>
                </actions>

                <!-- Display error message for unsupported OS and CPU architecture -->
                <actions>
                    <action type="shell_command">
                        echo "ERROR: This package only supports 64-bit systems running macOS or Linux"
                    </action>
                    <action type="shell_command">false</action>
                </actions>

                <!-- update $PATH environment variable -->
                <action type="set_environment">
                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
                </action>
            </actions_group>
        </install>
        <readme>
        
            This package contains the utilities for constructing
            `bigWig files &lt;https://genome.ucsc.edu/goldenpath/help/bigWig.html&gt;`_.
            The utilities were created by the
            `Genome Bioinformatics Group &lt;https://genome.ucsc.edu/staff.html&gt;`_
            at the UCSC Genomics Institute.

            The bigWig file format is designed to store dense continuous datasets
            and it is compatible with many genome browsers (e.g., UCSC Genome Browser,
            JBrowse, IGV).
        
        </readme>
    </package>
</tool_dependency>