Unable to access error while running docker container for GATK

Question

[Sara]

I am trying to use GATK via docker container, and the command to enter the container environment works fine (for gatk and other tools as well). Then, when I run the following command I would expect that gatk works fine:

Java -jar gatk

But I am getting this error:

Error: Unable to access jarfile GATK

Do you know what the problem is?

Answer 1

[iraun]

You can run gatk directly using the executable wrapper script called gatk. This executable will invoke the jar file. Try:

./gatk --help

[Sara]

iraun if that was possible I would do it. I have to use container due to the limitations I have on the hpc.

[GenoMax]

Can you clarify how you are doing the following?

command to enter the container environment works fine

[Sara]

GenoMax this is how I do it which works fine for other tools:

set +u; env - PATH="$PATH" SINGULARITYENV_TMP="$TMP" SINGULARITY_TMPDIR="$TMPDIR" SINGULARITY_CACHEDIR="/hpc/singularity_cache/" singularity shell -B /hpc:/hpc -B $TMPDIR:$TMPDIR docker://quay.io/biocontainers/gatk:3.5--6