annotate tool_dependencies.xml @ 0:cc6c4d6ebceb draft

Uploaded initial version developed by JJ and originally released as http://testtoolshed.g2.bx.psu.edu/view/jjohnson/package_mummer_3_23

<?xml version="1.0"?>
<tool_dependency>
    <package name="mummer" version="3.23">
        <install version="1.0">
            <actions>
                <action type="download_by_url">http://sourceforge.net/projects/mummer/files/mummer/3.23/MUMmer3.23.tar.gz</action>
                <action type="move_directory_files">
                    <source_directory>.</source_directory>
                    <destination_directory>$INSTALL_DIR</destination_directory>
                </action>
                <action type="shell_command">
                    cd $INSTALL_DIR; make;
                </action>
                <action type="set_environment">
                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/scripts</environment_variable>
                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable>
                </action>
            </actions>
        </install>
        <readme>
http://mummer.sourceforge.net/
MUMmer is a system for rapidly aligning entire genomes, whether in complete or draft form. For example, MUMmer 3.0 can find all 20-basepair or longer exact matches between a pair of 5-megabase genomes in 13.7 seconds, using 78 MB of memory, on a 2.4 GHz Linux desktop computer. MUMmer can also align incomplete genomes; it can easily handle the 100s or 1000s of contigs from a shotgun sequencing project, and will align them to another set of contigs or a genome using the NUCmer program included with the system. If the species are too divergent for a DNA sequence alignment to detect similarity, then the PROmer program can generate alignments based upon the six-frame translations of both input sequences. 
        </readme>
    </package>
</tool_dependency>