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.
define java to use in GATK4?
today I tried to run GATK4. But I ran into an issue. Just calling "gatk" looks fine, but when running "gatk --list" produces the following output.
java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=1 -jar /dsk/data1/ngs/bin/GATK/22.214.171.124/gatk-package-126.96.36.199-local.jar --help
Error: Invalid or corrupt jarfile /dsk/data1/ngs/bin/GATK/188.8.131.52/gatk-package-184.108.40.206-local.jar
Since now I have the command how GATK actually is started I replaced "java" with "java8" and everything works well.
So my question is, if there is an option, or config or anything, where I can define the path to my java8? I can't just switch to java8 as my main java since I'm working on a cluster, and the admins don't want it.
Thanks in advance,