Bug Bulletin: The recent 3.2 release fixes many issues. If you run into a problem, please try the latest version before posting a bug report, as your problem may already have been solved.

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

droazendroazen Posts: 51GATK Developer mod
edited June 24 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 BostonPosts: 3Member

    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!

Sign In or Register to comment.