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author jjohnson
date Fri, 04 Oct 2013 09:55:46 -0400
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<?xml version="1.0"?>
<tool_dependency>
    <package name="snpEff" version="3.3">
        <install version="1.0">
            <actions>
                <action type="download_by_url">http://sourceforge.net/projects/snpeff/files/snpEff_v3_3_core.zip</action>
                <action type="move_directory_files">
                    <source_directory>.</source_directory>
                    <destination_directory>$INSTALL_DIR</destination_directory>
                </action>
                <action type="set_environment">
                    <environment_variable name="SNPEFF_JAR_PATH" action="set_to">$INSTALL_DIR</environment_variable>
                </action>
                <action type="set_environment">
                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/scripts</environment_variable>
                </action>
            </actions>
        </install>
        <readme>

SnpEff ( http://snpeff.sourceforge.net/ )

"A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3.", Cingolani P, Platts A, Wang le L, Coon M, Nguyen T, Wang L, Land SJ, Lu X, Ruden DM. Fly (Austin). 2012 Apr-Jun;6(2):80-92. PMID: 22728672 [PubMed - in process]

This repository contains a tool_dependencies.xml file that downloads and installs SnpEff and SnpSift (SnpEff.jar and SnpSift.jar)

The install create an environment variable: SNPEFF_JAR_PATH that contains the path to the jar files.   Tools using this can generate a command line:
java -Xmx6G -jar \$SNPEFF_JAR_PATH/snpEff.jar eff -c \$SNPEFF_JAR_PATH/snpEff.config   ...

The snpEff.config file is also installed, which specifies the default location for installed SnpEff genome databases:
data_dir = ~/snpEff/data/

At this time there does not appear to be a way to edit that location during SnpEff installation.  Ideally it should be relative to the galaxy genome_data_path property set in universe_wsgi.ini, e.g.  genome_data_path/snpEff/data/

Another way to change the location of data_dir would be to create a symbolic link in the galaxy HOME directory:
ln -s genome_data_path/snpEff ~/snpEff

        </readme>
    </package>
</tool_dependency>