<!--
  ~ Copyright (c) 2012, 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
  ~ FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
  ~ OTHER DEALINGS IN THE SOFTWARE.
  -->

<ivy-module version="1.0">
  <info organisation="org.broadinstitute" module="Sting"/>
  <configurations defaultconfmapping="test->default">
    <conf name="default" description="the core dependencies for the GATK"/>
    <conf name="test" extends="default" description="external dependencies used for testing and metrics" />
    <conf name="scala" extends="default" description="the dependencies for scala"/>
    <conf name="queue" extends="scala" description="the dependencies for Queue"/>
  </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="0.9.5-RC2"/>

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

    <!-- Dependencies for the graph aligner -->  
    <dependency org="org.jgrapht" name="jgrapht-jdk1.5" rev="0.7.3"/>

    <!-- 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="2.0"/>
    <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="2.8.1"/>
    <dependency org="org.scala-lang" name="scala-library" rev="2.8.1"/>

    <!-- testing and evaluation dependencies -->
    <dependency org="org.testng" name="testng" rev="5.14.1" conf="test" />
    <dependency org="net.sourceforge.findbugs" name="findbugs" rev="1.3.2" conf="test"/>
    <dependency org="net.sourceforge.findbugs" name="findbugs-ant" rev="1.3.2" conf="test"/>
    <dependency org="net.sourceforge.findbugs" name="annotations" rev="1.3.2" conf="test"/>
    <dependency org="net.sourceforge.findbugs" name="jsr305" rev="1.3.2" conf="test"/>
    <dependency org="com.google.code.caliper" name="caliper" rev="1.0-SNAPSHOT" conf="test" />

    <!-- Contracts for Java and dependencies -->
    <dependency org="com.google.code.cofoja" name="cofoja" rev="1.0-20110609" />
    <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 Bjorn -->
    <dependency org="org.mongodb" name="mongo-java-driver" rev="2.7.3"/>

    <!-- 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>
