view tool_dependencies.xml @ 1:3480daf4ed27 draft

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<?xml version="1.0"?>
<tool_dependency>
    <package name="package_bowtie2" version="2.1.0">
        <repository changeset_revision="606d435a57a4" name="package_bowtie2_2_1_0" owner="devteam" toolshed="http://testtoolshed.g2.bx.psu.edu" />
    </package>
    <package name="fastq_screen" version="0.4.2">
        <install version="1.0">
            <actions>
                <action type="download_by_url">http://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/fastq_screen_v0.4.2.tar.gz</action>
                <action type="move_directory_files">
                    <source_directory>.</source_directory>
                    <destination_directory>$INSTALL_DIR</destination_directory>
                </action>
                <action type="set_environment">
                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR</environment_variable>
                </action>
            </actions>
        </install>
        <readme>
Galaxy wrapper for http://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/ from Simon Andrews.
Useful if you want to (eg) check your RNA sequence from a cell culture for contamination from (eg) Mycoplasma Genitalium, or if you have sequence from an unknown organism :(
Permanently set to use your Galaxy bowtie2 indices - expects Bowtie2 to be installed so the Galaxy package_bowtie2 is installed if it's not already there.

###WARNING### The fastq_screen perl script requires that the GD::Graph http://search.cpan.org/~bwarfield/GDGraph/Graph.pm module be installed.
Otherwise, NO plot will be created. This wrapper relies on the system perl - a proper Galaxy perl dependency is just too icky to think about.

Send code if you think otherwise.
        </readme>
    </package>

</tool_dependency>