If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!
Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
Instalation - Picard
I have downloaded Picard and htsjdk from gitgub as indicated in the documentation. However, when I go to the Picard root and type "ant", I get the following error:
[javac] picard/build.xml:537: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds
[javac] Compiling 407 source files to picard/htsjdk/classes
[javac] javac: invalid target release: 1.8
[javac] Usage: javac
[javac] use -help for a list of possible options
picard/build.xml:139: The following error occurred while executing this line:
picard/htsjdk/build.xml:96: The following error occurred while executing this line:
picard/build.xml:537: Compile failed; see the compiler error output for details.
I have tried to edit the JAVA6_HOME with /usr/lib/jvm/java-7-openjdk-amd64/lib/ and /usr/lib/jvm/java-6-openjdk-amd64/lib/. The same error persists.
Any help is appreciated.