How to access the picard and htsjdk repository (containing samtools-jdk, tribble, and variant)

droazendroazen Cambridge, MADev Posts: 51 ✭✭
edited June 2014 in Developer Zone

The picard repository on github contains all picard public tools. Libraries live under the htsjdk, which includes the samtools-jdk, tribble, and variant packages (which includes VariantContext and associated classes as well as the VCF/BCF codecs).

If you just need to check out the sources and don't need to make any commits into the picard repository, the command is:

git clone https://github.com/broadinstitute/picard.git

Then within the picard directory, clone the htsjdk.

cd picard
git clone https://github.com/samtools/htsjdk.git

Then you can attach the picard/src/java and picard/htsjdk/src/java directories in IntelliJ as a source directory (File -> Project Structure -> Libraries -> Click the plus sign -> "Attach Files or Directories" in the latest IntelliJ).

To build picard and the htsjdk all at once, type ant from within the picard directory. To run tests, type ant test

If you do need to make commits into the picard repository, first you'll need to create a github account, fork picard or htsjdk, make your changes, and then issue a pull request. For more info on pull requests, see: https://help.github.com/articles/using-pull-requests

Post edited by kshakir on

Comments

  • tguchtguch BostonMember Posts: 3

    I was actually able to find the VCF files in this path GenomeAnalysisTK-2.6-5\GenomeAnalysisTK-2.6-5-gba531bd\GenomeAnalysisTK\org\broadinstitute\variant\vcf and I changed the path location in the code, but it still can't seem to find or recognize it. Do you happen to know why this is and how to fix it?

    Thanks!

  • BobHarrisBobHarris earthMember Posts: 29

    To build picard and the htsjdk all at once, type ant from within the picard directory

    I am having no success with that -- the build tells me broadinstitute-picard-2a49ee2/htsjdk does not exist. I have tried building htsjdk, and as near as I call tell was successful. Do you know how I can tell the picard build where to find htsjdk?

    Sorry for multiple posts on this subject (e.g. gatkforums.broadinstitute.org/gatk/discussion/6826/picard-build-cant-find-htsjdk)

    Bob H

  • Geraldine_VdAuweraGeraldine_VdAuwera Administrator, Dev Posts: 10,287 admin

    Responding to your question in your first thread.

    Geraldine Van der Auwera, PhD

  • CarolCarol Member Posts: 44

    I typed ant and got a list of errors. how to solve the problem

    ant
    Buildfile: build.xml
    [exec] Result: 128

    set-htsjdk-version:

    write-version-property:
    [propertyfile] Updating property file: htsjdk/htsjdk.version.properties

    compile-htsjdk:

    clean:
    [delete] Deleting directory htsjdk/classes
    [delete] Deleting: htsjdk/htsjdk.version.properties

    write-version-property:
    [propertyfile] Creating new property file: htsjdk/htsjdk.version.properties

    init:

    compile-samtools:
    [mkdir] Created dir: htsjdk/classes
    [javac] build.xml:539: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds
    [javac] Compiling 412 source files to htsjdk/classes
    [javac] javac: invalid target release: 1.8
    [javac] Usage: javac

    [javac] use -help for a list of possible options
    

    BUILD FAILED
    build.xml:139: The following error occurred while executing this line:
    htsjdk/build.xml:96: The following error occurred while executing this line:
    build.xml:539: Compile failed; see the compiler error output for details.

    Total time: 0 seconds

    Issue · Github
    by Sheila

    Issue Number
    529
    State
    open
    Last Updated
    Assignee
    Array
  • pdexheimerpdexheimer Member, Dev Posts: 534 ✭✭✭✭

    @Carol -

    The line [javac] javac: invalid target release: 1.8 tells me that you're probably trying to use a jdk that is not 1.8. Try upgrading your jdk

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