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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
189 stars 53 forks source link

Docker issue with latest version #115

Closed emucaki closed 1 year ago

emucaki commented 1 year ago

I am trying to use "BamSurgeon" which uses SomaticSeq, however there is an error that reaches that step:

docker run --rm -v /home/data:/home/data -u ####:#### lethalfang/somaticseq:latest \ java ...

"Error response from daemon: failed to create shim task: OCI runtime create failed: runc create failed: unable to start container process: exec: "java": executable file not found in $PATH: unknown."

This problem does not happen when I use an older version of SomaticSeq: docker run --rm -v /home/data:/home/data -u ####:#### lethalfang/somaticseq:3.6.3 \ java ...

Just wanted to let you know.

litaifang commented 1 year ago

Thanks for letting me know. I put java back into lethalfang/somaticseq:latest.