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bioinform / somaticseq

An ensemble approach to accurately detect somatic mutations using SomaticSeq
http://bioinform.github.io/somaticseq/
BSD 2-Clause "Simplified" License
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singularity submit_SomaticSeq.sh code error ? #85

Closed gianfilippo closed 3 years ago

gianfilippo commented 4 years ago

Hi,

I got another error at the point where the submit_SomaticSeq.sh gets executed (the singularity version).

The error is /var/spool/slurmd/job9700596/slurm_script: line 14: docker: command not found

I checked the submit_SomaticSeq.sh code and it appears that at line 270 you have the following echo "docker pull lethalfang/somaticseq:${VERSION}" >> $out_script

the 'docker' is not recognized as command, of course.

I replaced it with the following echo "singularity pull docker://lethalfang/somaticseq:${VERSION}" >> $out_script

but I get the following error FATAL: Failed to initialize runtime engine: engine "" is not found

Clearly, what I did is not working. Can you please look into it ?

Thanks

litaifang commented 3 years ago

It seemed to work for me singularity pull docker://lethalfang/somaticseq:3.5.1, then singularity exec docker://lethalfang/somaticseq:3.5.1 ls -ls /opt/somaticseq.

gianfilippo commented 3 years ago

Hi,

this is now working. Most of my issues were related to singularity itself. They are not fully solved, but, at least, I can get it to work, with some effort Thanks