mounting folder in singularity -which directory to mount - docker

Question

My input files for the singularity program is not recognized (not found), which I think is due to the directory is not mounted within singularity.
I know that the mounting can be set by this command, but I am not sure which folders to mount.
export SINGULARITY_BIND="/somefolder:/somefolder"
How do I know which folders should be before and after the ":" sign in SINGULARITY_BIND?
I have set:
SINGULARITY_CACHEDIR=/mnt/scratch/username/software
where my singularity is stored.
My complete script:
export SINGULARITY_CACHEDIR=/mnt/scratch/username/software
export SINGULARITY_BIND="/home/username:/mnt/scratch/username"
OUTPUT_DIR="${PWD}/quickstart-output"
INPUT_DIR="${PWD}/quickstart-testdata"
BIN_VERSION="1.4.0"
# Run DeepVariant.
singularity run \
docker://google/deepvariant:"${BIN_VERSION}" \
/opt/deepvariant/bin/run_deepvariant \
--model_type=WGS \ **Replace this string with exactly one of the following [WGS,WES,PACBIO,HYBRID_PACBIO_ILLUMINA]**
--ref="${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_DIR}"/output.vcf.gz \
--output_gvcf="${OUTPUT_DIR}"/output.g.vcf.gz \
--intermediate_results_dir "${OUTPUT_DIR}/intermediate_results_dir" \ **Optional.
--num_shards=1 \ **How many cores the `make_examples` step uses. Change it to the number of CPU cores you have.**
My error:
singularity.clean.sh: line 23: --ref=/home/username/scratch/username/software/quickstart-testdata/ucsc.hg19.chr20.unittest.fasta: No such file or directory

Answer 1

If you want to bind mount your current working directory, you can use --bind $(pwd). If you want to bind mount your home directory, you can use --bind $HOME (note that singularity mounts the home directory by default). See the Singularity documentation for more information.
Based on your INPUT_DIR and OUTPUT_DIR, it seems like you can bind mount your current working directory. To do that, use --bind $(pwd). Note this argument goes before the name of the singularity container.
Just to be safe, also use --pwd $(pwd) to set the working directory in the container as the current working directory on the host.
OUTPUT_DIR="${PWD}/quickstart-output"
INPUT_DIR="${PWD}/quickstart-testdata"
BIN_VERSION="1.4.0"
singularity run --bind $(pwd) --pwd $(pwd) \
docker://google/deepvariant:"${BIN_VERSION}" \
/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="${OUTPUT_DIR}/output.vcf.gz" \
--output_gvcf="${OUTPUT_DIR}/output.g.vcf.gz" \
--intermediate_results_dir "${OUTPUT_DIR}/intermediate_results_dir" \
--num_shards=1
The syntax of the --bind argument is path-on-host:path-in-container. And using --bind path is shorthand for --bind path:path, which means the source path is mounted as the same path in the container. This can be very useful, because one does not have to rewrite paths and think in terms of the container's directories.