Add singularity usage to docs

Given that academic HPCs do not have root privileges it is not possible to run docker and one needs to use singularity. I think it would helpful to your user-base if you added a section on singularity to either the deepvariant-quick-start.md or README.md.

I had never used containers before today so the following would have been very helpful for me getting your tool up-and-running quicker:

Download an existing container from Docker Hub

singularity build deepvariant.simg docker://google/deepvariant

Run Deep Variant with Singularity in one command

singularity -s exec -B /usr/lib/locale/:/usr/lib/locale/  \
  deepvariant.simg \
  /opt/deepvariant/bin/run_deepvariant \
  --model_type=WGS \
  --ref=${INPUT_DIR}/ucsc.hg19.chr20.unittest.fasta \
  --reads=${INPUT_DIR}/NA12878_S1.chr20.10_10p1mb.bam \
  --regions "chr20:10,000,000-10,010,000" \
  --output_vcf=output.vcf.gz \
  --output_gvcf=output.g.vcf.gz 

Respectfully, Matthew

[pichuan]

@moldach Actually, I think I might know the problem. Does your OUTPUT_DIR exist?

I suggest you add a line below:

OUTPUT_DIR="${PWD}/quickstart-output"
mkdir -p ${OUTPUT_DIR}

to first ensure the directory is created.

[pichuan]

Hi @moldach somehow your logs above have a lot of spaces in the middle, making it hard to read.

It seems like the last step was looking for /scratch/moldach/bin/quickstart-output/output.vcf.gz but couldn’t find it.

I’ll walk through the steps again to see if I can reproduce your error, but meanwhile, can you try:

singularity run -B $PWD,/usr/lib/locale/ \

instead of

singularity run -B /usr/lib/locale/:/usr/lib/locale/  \

And see if it works for you? Thanks.