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

Cambridge, MAPosts: 51Dev ✭✭
edited June 2014

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
Tagged:

• 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!

• earthPosts: 29Member

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 Van der Auwera, PhD

• Posts: 44Member

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 January 28 by Sheila

Issue Number
529
State
open
Last Updated
Assignee
Array
• Posts: 541Member, Dev ✭✭✭✭

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