comparison tool_dependencies.xml @ 0:3645871df985 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_subread_1_4_6_p5 commit 4f89482db4edf80fb5cd8dfa0e661761b032817c

0:3645871df985

<?xml version="1.0"?>
<tool_dependency>
    <package name="subread" version="1.4.6p5">
        <install version="1.0">
            <actions>
                <action type="download_by_url"
                    sha256sum="8292ff6420356a5560c4a07f876f785622abbcae9fa54ef6750d102f40f78315">http://downloads.sourceforge.net/project/subread/subread-1.4.6-p5/subread-1.4.6-p5-source.tar.gz</action>
                <action type="shell_command"><![CDATA[
                    cd src/ && make -f Makefile.Linux
                ]]></action>
                <action type="move_directory_files">
                    <source_directory>bin</source_directory>
                    <destination_directory>$INSTALL_DIR/bin</destination_directory>
                </action>
                <action type="set_environment">
                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin/utilities</environment_variable>
                </action>
            </actions>
        </install>
        <readme>
            Downloads and installs the Subread package containing:
             - exactSNP
             - featureCounts
             - subindel
             - subjunc
             - subread-align
             - subread-buildindex

            with the corresponding utilities:
              * coverageCount
              * globalReassembly
              * propmapped
              * qualityScores
              * removeDup
              * subread-fullscan
              * subtools

            http://subread.sourceforge.net/
        </readme>
    </package>
</tool_dependency>