This site is now read-only. You can find our new documentation site and support forum for posting questions here.
Be sure to read our welcome blog!
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,