Skip to content


Subversion checkout URL

You can clone with
Download ZIP
Tag: 1.3
Fetching contributors…

Cannot retrieve contributors at this time

87 lines (68 sloc) 4.13 KB
<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"/>
<dependencies defaultconf="default">
<dependency org="net.sf" name="sam" rev="latest.integration"/>
<dependency org="net.sf" name="picard" rev="latest.integration"/>
<dependency org="" 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=""/>
<dependency org="org.simpleframework" name="simple-xml" rev="2.0.4"/>
<dependency org="org.apache.bcel" name="bcel" rev="5.2"/>
<dependency org="org.yaml" name="snakeyaml" rev="1.7"/>
<!-- Dependencies for reflections mvn repository -->
<dependency org="org.reflections" name="reflections" rev="0.9.5-RC2"/>
<!-- Matrix package from -->
<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="2.0"/>
<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="" name="jna" rev="3.2.7"/>
<!-- Dependencies for S3 support -->
<dependency org="" name="jets3t" rev="0.8.0"/>
<!-- 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="" name="caliper" rev="1.0-SNAPSHOT" conf="test" />
<!-- Contracts for Java and dependencies -->
<dependency org="" 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="2.0.2" />
<!-- 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.*" />
Jump to Line
Something went wrong with that request. Please try again.