Parabricks with Cudo Compute
Prerequisites
- Create a project and add an SSH key
- Optionally download CLI tool
- Choose a VM with an NVIDIA GPU and Configure
- Use the Ubuntu 22.04 + Nvidia drivers + Docker image (in CLI tool type
-image ubuntu-nvidia-docker
)
Running Parabricks with Docker
docker pull nvcr.io/nvidia/clara/clara-parabricks:4.0.0-1
NGC tags can be found here More tutorials [here] (https://docs.nvidia.com/clara/parabricks/4.0.0/Tutorials.html)
Sample walkthrough
Download the sample data
wget -O parabricks_sample.tar.gz \
"https://s3.amazonaws.com/parabricks.sample/parabricks_sample.tar.gz"
Extract the data
tar xvf parabricks_sample.tar.gz
docker run \
--gpus all \
--rm \
--volume $(pwd):/workdir \
--volume $(pwd):/outputdir \
nvcr.io/nvidia/clara/clara-parabricks:4.0.0-1 \
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
[Parabricks Options Mesg]: Checking argument compatibility
[Parabricks Options Mesg]: Automatically generating ID prefix
[Parabricks Options Mesg]: Read group created for /workdir/parabricks_sample/Data/sample_1.fq.gz and
/workdir/parabricks_sample/Data/sample_2.fq.gz
[Parabricks Options Mesg]: @RG\tID:HK3TJBCX2.1\tLB:lib1\tPL:bar\tSM:sample\tPU:HK3TJBCX2.1
[PB Info 2022-Oct-14 09:54:15] ------------------------------------------------------------------------------
[PB Info 2022-Oct-14 09:54:15] || Parabricks accelerated Genomics Pipeline ||
...
On a 4x Nvidia A4000 VM this process takes around 1m 30s
To view the results run:
apt install samtools
samtools view fq2bam_output.bam
HWI-D00127:570:HK3TJBCX2:2:2215:1035:92366 77 * 0 0 * * 0 0 NAAAGACGGAGAGCGCCAACGGCGTCCATCTCGAAGGAGTCGCCAGCGATAACCGGAGTAGTTGAAATGGTAATAAGACGACCAATCTGACCAGCAAGGAAGCCAAGATGGGAAA #<
For more help on Parabricks see the NVIDIA docs
Want to learn more?
You can learn more about using Parabricks on Cudo Compute by contacting us. Or you can just get started right away!