How to run Singularity

[moldach]

I'm using an academic HPC so the use of docker is not allowed due to security concerns.

I would like to know how I can run hap.py using singularity:

I'm following the [deepvariant] tutorial and have tried the following without luck.

singularity pull docker://pkrusche/hap.py

singularity run -it \
  -v "${INPUT_DIR}":"/input" \
  -v "${OUTPUT_DIR}:/output" \
  pkrusche/hap.py /opt/hap.py/bin/hap.py \
  /input/test_nist.b37_chr20_100kbp_at_10mb.vcf.gz \
  /output/output.vcf.gz \
  -f "/input/test_nist.b37_chr20_100kbp_at_10mb.bed" \
  -r "/input/ucsc.hg19.chr20.unittest.fasta" \
  -o "/output/happy.output" \
  --engine=vcfeval \
  -l chr20:10000000-10010000

What should the code would look like to run?

[kunstner]

Hi @moldach,

the following lines of code should work for a singularity container

# fetch latest version
singularity pull docker://pkrusche/hap.py

# set number of threads, reference fasta file and bed file from exome capture kit
THREADS=$(nproc)
REF=/data/lied_sb_tumor_01/_genomes/somatic-b37_Homo_sapiens_assembly19.fasta
BEDFILE=/data/sb_service_01/128_TNAMSE_RalfWerner/data/ssHAEv7_2019_07_19_noChr.bed
 
# run singularity container
# haplotype caller as 'ground truth' and deepvariant calls as test
singularity exec hap.py_latest.sif /opt/hap.py/bin/hap.py \
  --false-positives $BEDFILE \
  --reference $REF \
  --report-prefix happy.output \
  --engine=vcfeval \
  --threads $THREADS \
  ../04_haplotypecaller/DX196319.left.vcf.gz \
  ../03_deepvariant/DX196319.dv.left.vcf.gz

Here, I used GATK haplotype caller output as ground truth and tested deepvariant calls.

Hope that helps.

Best,
Axel

[netwon123]

i want to know where is /opt/hap.py/bin/hap.py

[kunstner]

i want to know where is /opt/hap.py/bin/hap.py

It is inside the singularity container.

//axel

[netwon123]

Sorry sir, I just get the hap.py_latest.sif after using 'singularity pull docker://pkrusche/hap.py'. i don't get the hap.py under path '/opt'. could u tell me detailed explanation? thanks u very much.

[kunstner]

It is a path inside the singularity container. Singularity executes this binary inside the container. You just need the sif file. Everyting else is inside the sif file. Nothing to worry about.

[netwon123]

It is a path inside the singularity container. Singularity executes this binary inside the container. You just need the sif file. Everyting else is inside the sif file. Nothing to worry about.

i got it. Thanks! Just use it directly.