bc lacking in dockerhub image gridss/virusbreakend:2.13.2

[splaisan]

Dear,

I installed the docker image gridss/virusbreakend:2.13.2 (https://hub.docker.com/r/gridss/virusbreakend/tags) and ran it to discover that bc was not installed in the docker image, causing two error messages at the end of the code.

/opt/gridss/virusbreakend: line 857: bc: command not found
/opt/gridss/virusbreakend: line 871: bc: command not found

The docker file in the current repo doe snot list bc either.

after running the image in -it and installing bc, then creating a new copy the error goes away

Best regards

PS: I also noticed that metric files are written in the current folder although I gave a path to the vcf file elsewhere, can I correct thsi to have the metric files saved next to the vcf?

The RM folder is also created in the current folder and should be better placed in the workingdir path, can I set this somewhere?

# /workingdir points to a tmp folder not being /tmp

  docker run --rm \
    --user "$(id -u):$(id -g)" \
    -v "${curdir}/sv_results/tmpfiles":"/workingdir" \
    -v "${virusbreakenddb}":"/dbpath" \
    -v "${curdir}":"/data" \
    gridss/virusbreakend:2.13.2-with-bc virusbreakend \
      -t "${nthr}" \
      -w /workingdir \
      --db /dbpath \
      -o "/data/sv_results/raw_virusbreakend_results/${label}_raw_virusbreakend.vcf" \
      --host human \
      -r "/data/${hostref}" \
      --minreads 10 \
      --minviralcoverage 5 \
      --force \
      "/data/${inbam}" \