comparison tool_dependencies.xml @ 1:9b8e2a158073 draft

Fix typo in unified_genotyper.xml, add dir path in tool_dependencies.xml

0:74c05070a3f8

<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>
                <action type="move_file">
                    <source>GenomeAnalysisTKLite.jar</source>
                    <destination>$INSTALL_DIR/GenomeAnalysisTK.jar</destination>
                </action>
                <action type="set_environment">
                    <environment_variable name="GATK2_PATH" action="set_to">$INSTALL_DIR</environment_variable>
                </action>

1:9b8e2a158073

<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-2.2-2-gd3f5a5e/
                     which common_util.py tar_extraction_directory() does not find
                     so the move file must contain the GenomeAnalysisTKLite-2.2-2-gd3f5a5e dir path
                 -->
                <action type="move_file">
                    <source>GenomeAnalysisTKLite-2.2-2-gd3f5a5e/GenomeAnalysisTKLite.jar</source>
                    <destination>$INSTALL_DIR/GenomeAnalysisTK.jar</destination>
                </action>
                <action type="set_environment">
                    <environment_variable name="GATK2_PATH" action="set_to">$INSTALL_DIR</environment_variable>
                </action>