comparison tool_dependencies.xml @ 15:35c6289faeff draft

Update tool_dependecies to GenomeAnalysisTKLite-2.2-8-g99996f2.tar.bz2

14:d73c92a7b0ea

<?xml version="1.0"?>
<tool_dependency>
    <package name="gatk" version="2.2">
        <install version="1.0">
            <actions>
                <action type="download_by_url">ftp://ftp.broadinstitute.org/pub/gsa/GenomeAnalysisTK/GenomeAnalysisTKLite-latest.tar.bz2</action>
                <!-- this expands into GenomeAnalysisTKLite-2.2-3-g63dddfb/
                     which common_util.py tar_extraction_directory() does not find
                     so the move file must contain the GenomeAnalysisTKLite-2.2-3-g63dddfb dir path
                 -->
                <action type="move_file">
                    <source>GenomeAnalysisTKLite-2.2-3-g63dddfb/GenomeAnalysisTKLite.jar</source>
                    <destination>$INSTALL_DIR</destination>
                </action>
                <action type="shell_command">ln -s GenomeAnalysisTKLite.jar GenomeAnalysisTK.jar</action>
                <action type="move_file">
                    <source>GenomeAnalysisTK.jar</source>

15:35c6289faeff

<?xml version="1.0"?>
<tool_dependency>
    <package name="gatk" version="2.2">
        <install version="1.0">
            <actions>
                <action type="download_by_url">ftp://ftp.broadinstitute.org/pub/gsa/GenomeAnalysisTK/GenomeAnalysisTKLite-2.2-8-g99996f2.tar.bz2</action>
                <action type="move_file">
                    <source>GenomeAnalysisTKLite.jar</source>
                    <destination>$INSTALL_DIR</destination>
                </action>
                <action type="shell_command">ln -s GenomeAnalysisTKLite.jar GenomeAnalysisTK.jar</action>
                <action type="move_file">
                    <source>GenomeAnalysisTK.jar</source>