<?xml version="1.0" encoding="UTF-8"?>
<!--
  ~ Copyright (c) 2011, The Broad Institute
  ~
  ~ Permission is hereby granted, free of charge, to any person
  ~ obtaining a copy of this software and associated documentation
  ~ files (the "Software"), to deal in the Software without
  ~ restriction, including without limitation the rights to use,
  ~ copy, modify, merge, publish, distribute, sublicense, and/or sell
  ~ copies of the Software, and to permit persons to whom the
  ~ Software is furnished to do so, subject to the following
  ~ conditions:
  ~
  ~ The above copyright notice and this permission notice shall be
  ~ included in all copies or substantial portions of the Software.
  ~ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
  ~ EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
  ~ OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
  ~ NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
  ~ HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
  ~ WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
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<package name="Queue">
    <version file="StingText.properties" property="org.broadinstitute.sting.queue.version" />
    <executable name="Queue">
        <main-class name="org.broadinstitute.sting.queue.QCommandLine" />
        <resource-bundle file="StingText.properties" />
        <dependencies>
            <!-- Queue -->
            <package name="org.broadinstitute.sting.queue.**" />

            <!-- Pipeline + Utils -->
            <package name="org.broadinstitute.sting.pipeline.**" />
            <package name="org.broadinstitute.sting.utils.**" />

            <!-- Scala -->
            <package name="scala.**" />

            <!-- Picard -->
            <package name="net.sf.picard.**" />
            <package name="edu.mit.broad.picard.**" />

            <!-- JavaMail -->
            <package name="javax.activation.**" />
            <package name="javax.mail.**" />
            <package name="com.sun.activation.**" />
            <package name="com.sun.mail.**" />
            <file path="META-INF/javamail.charset.map" />
            <file path="META-INF/javamail.default.address.map" />
            <file path="META-INF/javamail.default.providers" />
            <file path="META-INF/mailcap" />
            <file path="META-INF/mailcap.default" />
            <file path="META-INF/mimetypes.default" />

            <!-- JNA, including embedded native libraries -->
            <dir name="com/sun/jna" />

            <!-- Contracts for Java -->
            <package name="com.google.java.contract.**" />

            <!-- snpEff -->
            <package name="ca.mcgill.mcb.pcingola.**" />
            <file path="snpEff_genes.ftl" />
            <file path="snpEff_summary.ftl" />
            
            <!-- R scripts -->
            <dir name="org/broadinstitute/sting/queue" includes="**/*.R" />

        </dependencies>
        <modules>
            <module file="GATKEngine.xml"/>
            <module file="AnalyzeCovariates.xml"/>
        </modules>
    </executable>
    <release>
        <executable directory="/humgen/gsa-hpprojects/Queue/bin" symlink="current" />
        <archive directory="/web/ftp/pub/gsa/Queue" symlink="Queue-latest.tar.bz2" />
    </release>
</package>
