Comments (2)
Hi @potter-s
Our docker image is already built with root account only however PATH is set to be usable by all users so if you wish to keep user priviledges after execution you may add -u $UID:$GID
parameter to docker command line therefore the container will run using your user permissions.
This has a catch of course. Temporary folders must be set where your user has RWX permissions therefore we want users to pay attention to that. There is a writing that we posted a while ago which you may refer to for setting up your temporary files for GATK workflows.
How to setup temporary folder for GATK local executtion
For some of the tools such as gCNV or CNN you may need to setup additional environment variables to locate python compilation directory to a place where you have read and write permissions.
I hope this helps.
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Related Issues (20)
- ApplyVQSR Exception thrown at a/some variation site(s) after INDEL VQSR
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