Clara Parabricks

Clara Parabricks is available at MSI via a singularity image (see here for documentation on singularity at MSI). It expects NVIDIA GPUs to be available when it runs, so you will want to make sure you are using it on one of MSI's GPU partitions on Mangi or Agate (see here for a listing of available partitions). 

An example Parabricks command might look like the following. This example command is adapted from the Docker-based FQ2BAM tutorial provided by NVIDIA. You will need to have followed their instructions for downloading and extracting the data from the Getting the Sample Data step of their tutorial before running these commands.

module load singularity
singularity run --nv \
    -B $(pwd):/workdir \
    -B $(pwd):/outputdir \
    --pwd /workdir \
    /software/singularity-images/clara-parabricks/4.0.0-1.sif \
    pbrun fq2bam \
    --ref /workdir/parabricks_sample/Ref/Homo_sapiens_assembly38.fasta \
    --in-fq /workdir/parabricks_sample/Data/sample_1.fq.gz /workdir/parabricks_sample/Data/sample_2.fq.gz \
    --out-bam /outputdir/fq2bam_output.bam

•  `--nv` lets singularity detect and use the NVIDIA GPUs available on the current host
• `-B $(pwd):/input_data` mounts your current working directory on MSI to the path `/input_data` inside the container
• `--pwd /workdir` tells singularity to run commands using `/workdir` inside the container as the working directory