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Initial commit of test for FastQC with installation of the java stuff
author fubar
date Mon, 03 Jun 2013 20:30:24 -0400
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children 45cd27a2ad5c
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<?xml version="1.0"?>
<tool_dependency>
    <set_environment version="1.0">
        <environment_variable name="FASTQC_INSTALL_PATH" action="set_to">$INSTALL_DIR/jars/FastQC</environment_variable>   
    </set_environment>
    <package name="FastQC" version="0.10.1">
        <install version="1.0">
            <actions>
                <action type="download_by_url">http://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.10.1.zip</action>
                <action type="move_directory_files">
                    <source_directory>FastQC</source_directory>
                    <destination_directory>$INSTALL_DIR/jars</destination_directory>
                </action>
                <action type="shell_command">chmod ugo+x $INSTALL_DIR/jars/FastQC/fastqc</action>
            </actions>
        </install>
        <readme>You need a working unzip command line executable to install this tool and a suitable working Java run time environment 
                available to all potential execution nodes for this tool to work.
                Please see http://www.bioinformatics.babraham.ac.uk/projects/fastqc for all FastQC documentation</readme>
    </package>
</tool_dependency>