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<?xml version="1.0"?>
<tool_dependency>
    <package name="crest" version="1.0.1">
        <install version="1.0">
            <actions>
                <action type="download_by_url">ftp://ftp.stjude.org/pub/software/CREST/CREST.tgz</action>
                <action type="move_directory_files">
                    <source_directory>.</source_directory>
                    <destination_directory>$INSTALL_DIR</destination_directory>
                </action>
                <action type="set_environment">
                    <environment_variable name="CREST_DIRECTORY" action="set_to">$INSTALL_DIR</environment_variable>
                </action>
                <action type="set_environment">
                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable>
                </action>
            </actions>
        </install>
        <readme>
CREST

CREST (Clipping Reveals Structure) is a new algorithm for detecting genomic structural variations at base-pair resolution using next-generation sequencing data. Please cite the following article:

Wang J, Mullighan CG, Easton J, Roberts S, Heatley SL, Ma J, Rusch MC, Chen K, Harris CC, Ding L, Holmfeldt L, Payne-Turner D, Fan X, Wei L, Zhao D, Obenauer JC, Naeve C, Mardis ER, Wilson RK, Downing JR and Zhang J. CREST maps somatic structural variation in cancer genomes with base-pair resolution (2011). Nature Methods.

The source code can be downloaded here and used according to the terms of the GNU General Public License (GPL), version 2 or later. 

Users will need to obtain the BLAT and CAP3 programs separately to use CREST; BLAT and CAP3 are free for academic use but require licensing fees for commercial use. The open source BioPerl and SAMtools libraries are also needed to use CREST.

http://www.stjuderesearch.org/site/lab/zhang
        </readme>
    </package>

</tool_dependency>