What does the -B mean when running deepvariant as a singularity container?

[amyhouseman]

This might be an obvious question but i cannot work it out, what does the -B mean?

For example from your singularity guide:

singularity run **-B** /usr/lib/locale/:/usr/lib/locale/ \
  docker://google/deepvariant:"${BIN_VERSION}" \
  /opt/deepvariant/bin/run_deepvariant \

Also, if using a singularity container would you use it like this (fake link to the container):

wget https://containers/deepvariant_1.3.0.sif  
module load singularity

singularity run deepvariant_1.3.0.sif -B  --model_type=WES -ref=PolyposisExomeAnalysis/bwa/index/HumanRefSeq/GRCh38_latest_genomic.fna
--reads=PolyposisExomeAnalysis/samtoolssort/{}PE_samtoolssorted.bam
--output_vcf=PolyposisExomeAnalysis/deepvariant/vcf/PE_output.vcf.gz 
--output_gvcf=PolyposisExomeAnalysis/deepvariant/gvcf/PE_output.vcf.gz
--intermediate_results_dir PolyposisExomeAnalysis/deepvariant/intermediateresults/

Sorry, still figuring it out! Thanks, Amy

[akolesnikov]

From the help page of Singularity Container link:

-B, --bind strings           a user-bind path specification.  spec has the format src[:dest[:opts]], where src and dest are outside and inside paths.  If dest is not given, it is set equal to src.  Mount options ('opts') may be specified as 'ro' (read-only) or 'rw' (read/write, which is the default). Multiple bind paths can be given by a comma separated list.

Basically, this option binds your local directory to the directory inside a container.

Also see https://github.com/google/deepvariant/blob/r1.3/docs/deepvariant-quick-start.md#notes-on-singularity