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 cegma-test \
-v `pwd`/sequence:/in \
-v `pwd`/cegma:/out \
-e ASSEMBLY=scaffolds.fa.gz \
-e THREADS=16 \
genomehubs/cegma:latest
Writes scaffolds.fa.completeness_report.txt and scaffolds.fa.cegma.gff to the directoy mounted at /out.