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Unable to access error while running docker container for GATK

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?

gatk docker
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written by Sara Sara

1 answer

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

./gatk --help
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written by iraun iraun

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

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written by Sara Sara

Can you clarify how you are doing the following?

command to enter the container environment works fine

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written by GenoMax GenoMax

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
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written by Sara Sara

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