genomehubs/cegma
Container to run CEGMA optimised for GenomeHubs
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CEGMA docker container built from hub.docker.com/r/robsyme/cegma-docker with modifications to make it easier to use as a GenomeHubs container by running as UID 1000, separating input and output directories and renaming output files.
docker run -d \
--name genomehubs-cegma \
-v `pwd`/sequence:/in \
-v `pwd`/cegma:/out \
-e ASSEMBLY=scaffolds.fa.gz \
genomehubs/cegma:latest
Writes scaffolds.fa.completeness_report.txt
and scaffolds.fa.cegma.gff
to the directoy mounted at /out
.
docker pull genomehubs/cegma