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cancerit / BRASS

Breakpoints via assembly - Identifies breaks and attempts to assemble rearrangements in whole genome sequencing data.
GNU Affero General Public License v3.0
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docker container gives errors when run from singularity #92

Closed cboursnell closed 4 years ago

cboursnell commented 4 years ago

I am trying to use the docker image from quay.io/wtsicgp/brass on our hpc. I have run singularity build --remote brass.sif docker://quay.io/wtsicgp/brass:v6.3.0 and then singularity exec brass.sif brass.pl I get this error message: IPC::System::Simple required for Fatalised/autodying system() at /opt/wtsi-cgp/bin/brass.pl line 40. main::BEGIN() called at /opt/wtsi-cgp/bin/brass.pl line 40 eval {...} called at /opt/wtsi-cgp/bin/brass.pl line 40 BEGIN failed--compilation aborted at /opt/wtsi-cgp/bin/brass.pl line 40. There is little information in the README or on the wiki about running brass with the docker image. Could you help with fixing this please?

keiranmraine commented 4 years ago

Under singularity use --cleanenv otherwise it passes in the wrapping environment and clobbers the ones set within the container.

I reported this issue to singularity and it appears a fix for this is either released or soon to be:

https://github.com/sylabs/singularity/issues/3331#issuecomment-494519266