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Adding Third-party Dependencies

The GATK build system uses the Ivy dependency manager to make it easy for our users to add additional dependencies. Ivy can pull the latest jars and their dependencies from the Maven repository, making adding or updating a dependency as simple as adding a new line to the ivy.xml file.

If your tool is available in the maven repository, add a line to the ivy.xml file similar to the following:

<dependency org="junit" name="junit" rev="4.4" />

If you would like to add a dependency to a tool not available in the maven repository, please email gsahelp@broadinstitute.org

Updating SAM-JDK and Picard

Because we work so closely with the SAM-JDK/Picard team and are critically dependent on the code they produce, we have a special procedure for updating the SAM/Picard jars. Please use the following procedure to when updating sam-*.jar or picard-*.jar.

  • Download and build the latest versions of Picard public and Picard private (restricted to Broad Institute users) from their respective svns.

  • Get the latest svn versions for picard public and picard private by running the following commands:

    svn info $PICARD_PUBLIC_HOME | grep "Revision" svn info $PICARD_PRIVATE_HOME | grep "Revision"

Updating the Picard public jars

  • Rename the jars and xmls in $STING_HOME/settings/repository/net.sf to {picard|sam}-$PICARD_PUBLIC_MAJOR_VERSION.$PICARD_PUBLIC_MINOR_VERSION.PICARD_PUBLIC_SVN_REV.{jar|xml}

  • Update the jars in $STING_HOME/settings/repository/net.sf with their newer equivalents in $PICARD_PUBLIC_HOME/dist/picard_lib.

  • Update the xmls in $STING_HOME/settings/repository/net.sf with the appropriate version number ($PICARD_PUBLIC_MAJOR_VERSION.$PICARD_PUBLIC_MINOR_VERSION.$PICARD_PUBLIC_SVN_REV).

Updating the Picard private jar

  • Create the picard private jar with the following command:

    ant clean package -Dexecutable=PicardPrivate -Dpicard.dist.dir=${PICARD_PRIVATE_HOME}/dist

  • Rename picard-private-parts-*.jar in $STING_HOME/settings/repository/edu.mit.broad to picard-private-parts-$PICARD_PRIVATE_SVN_REV.jar.

  • Update picard-private-parts-*.jar in $STING_HOME/settings/repository/edu.mit.broad with the picard-private-parts.jar in $STING_HOME/dist/packages/picard-private-parts.

  • Update the xml in $STING_HOME/settings/repository/edu.mit.broad to reflect the new revision and publication date.

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Comments (4)

Hi, this took me a while to debug, so I'm posting the solution here. I started by downloading a clean copy of GATK core platform from GitHub. When I first tried building by running ant, I got the compiler errors below. The reason turned out to be that an unrelated jar (gsea2-2.0.12.jar) was on my CLASSPATH (this is from another Broad tool I've been using - Gene Set Enrichment Analysis). gsea2-2.0.12.jar apparently contains outdated versions of apache math and io packages which conflict with the GATK versions. Taking this jar off my CLASSPATH fixed the issue.

-Ben

Ps. the compiler errors were:

gatk.compile.internal.source:
    [javac] Compiling 681 source files to /prog/GATK/gatk_platform_git/build/java/classes
    [javac] /prog/GATK/gatk_platform_git/public/java/src/org/broadinstitute/sting/commandline/ParsingEngine.java:260: error: incompatible types
    [javac]         for (String line: FileUtils.readLines(file))
    [javac]                                              ^
    [javac]   required: String
    [javac]   found:    Object
    [javac] /prog/GATK/gatk_platform_git/public/java/src/org/broadinstitute/sting/utils/MannWhitneyU.java:50: error: no suitable constructor found for NormalDistributionImpl(double,double,double)
    [javac]     private static NormalDistribution APACHE_NORMAL = new NormalDistributionImpl(0.0,1.0,1e-2);
    [javac]                                                       ^
    [javac]     constructor NormalDistributionImpl.NormalDistributionImpl() is not applicable
    [javac]       (actual and formal argument lists differ in length)
    [javac]     constructor NormalDistributionImpl.NormalDistributionImpl(double,double) is not applicable
    [javac]       (actual and formal argument lists differ in length)
    [javac] Note: Some input files use or override a deprecated API.
    [javac] Note: Recompile with -Xlint:deprecation for details.
    [javac] Note: Some input files use unchecked or unsafe operations.
    [javac] Note: Recompile with -Xlint:unchecked for details.
    [javac] 2 errors

BUILD FAILED
/prog/GATK/gatk_platform_git/build.xml:454: Compile failed; see the compiler error output for details.