ivy.xml

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<ivy-module version="1.0">
    <info organisation="org.broadinstitute" module="Sting"/>
    <configurations>
        <conf name="default" description="the core dependencies for the GATK"/>
    </configurations>
    <dependencies defaultconf="default">
        <dependency org="net.sf" name="sam" rev="latest.integration"/>
        <dependency org="net.sf" name="picard" rev="latest.integration"/>
        <dependency org="edu.mit.broad" name="picard-private-parts" rev="latest.integration"/>

        <!-- Tribble -->
        <dependency org="org.broad" name="tribble" rev="latest.integration"/>

        <dependency org="log4j" name="log4j" rev="1.2.15"/>
        <dependency org="javax.mail" name="mail" rev="1.4.4"/>
        <dependency org="colt" name="colt" rev="1.2.0"/>
        <!-- <dependency org="jboss" name="javassist" rev="3.7.ga"/> -->
        <dependency org="org.simpleframework" name="simple-xml" rev="2.0.4"/>
        <dependency org="org.apache.bcel" name="bcel" rev="5.2"/>

        <!-- Dependencies for reflections mvn repository -->
        <dependency org="org.reflections" name="reflections" rev="0.9.8"/>
        <dependency org="org.slf4j" name="slf4j-log4j12" rev="1.6.1"/>

        <!-- Matrix package from math.nist.gov -->
        <dependency org="gov.nist" name="Jama" rev="1.0.2"/>

        <!-- Dependencies for the graph aligner -->
        <dependency org="net.sf.jgrapht" name="jgrapht" rev="0.8.3"/>

        <!-- Dependencies for the html walker documention -->
        <dependency org="org.freemarker" name="freemarker" rev="2.3.18"/>

        <!-- Commons Dependencies -->
        <dependency org="org.apache.commons" name="commons-email" rev="1.2"/>
        <dependency org="org.apache.commons" name="commons-jexl" rev="2.1.1"/>
        <dependency org="commons-lang" name="commons-lang" rev="2.5"/>
        <dependency org="commons-logging" name="commons-logging" rev="1.1.1"/>
        <dependency org="commons-io" name="commons-io" rev="2.1"/>
        <dependency org="org.apache.commons" name="commons-math" rev="2.2"/>

        <!-- Lucene core utilities -->
        <!-- <dependency org="org.apache.lucene" name="lucene-core" rev="3.0.3"/> -->

        <!-- Dependencies for LSF, DRMAA, and other C libraries -->
        <dependency org="net.java.dev.jna" name="jna" rev="3.2.7"/>

        <!-- Dependencies for amazon.com S3 support -->
        <dependency org="net.java.dev.jets3t" name="jets3t" rev="0.8.1"/>

        <!-- Dependencies for GridEngine -->
        <dependency org="net.sf.gridscheduler" name="drmaa" rev="latest.integration"/>

        <!-- Scala dependancies -->
        <dependency org="org.scala-lang" name="scala-compiler" rev="2.9.2"/>
        <dependency org="org.scala-lang" name="scala-library" rev="2.9.2"/>

        <!-- testing and evaluation dependencies -->
        <dependency org="org.testng" name="testng" rev="5.14.1"/>
        <dependency org="org.uncommons" name="reportng" rev="1.1.2"/>
        <dependency org="com.google.code.caliper" name="caliper" rev="1.0-SNAPSHOT"/>

        <!-- Contracts for Java and dependencies -->
        <dependency org="com.google.code.cofoja" name="cofoja" rev="1.0-r139"/>
        <dependency org="asm" name="asm-all" rev="3.3.1"/>

        <!-- POI, for reading pipeline files -->
        <dependency org="org.apache.poi" name="poi" rev="3.8-beta3"/>
        <dependency org="org.apache.poi" name="poi-ooxml" rev="3.8-beta3"/>

        <!-- snpEff annotator for pipelines -->
        <dependency org="net.sf.snpeff" name="snpeff" rev="2.0.5"/>

        <!-- MongoDB for the GXDB project -->
        <dependency org="org.mongodb" name="mongo-java-driver" rev="2.7.3"/>

        <!-- GSON and HTTP for talking to the REST API on Vanilla Forums -->
        <dependency org="com.google.code.gson" name="gson" rev="2.2.2"/>
        <dependency org="org.apache.httpcomponents" name="httpclient" rev="4.1.1"/>

        <!-- Exclude dependencies on sun libraries where the downloads aren't available but included in the jvm. -->
        <exclude org="javax.servlet"/>
        <exclude org="javax.jms"/>
        <exclude org="com.sun.*"/>
    </dependencies>
</ivy-module>