[Parabricks][v4.0] how to run Parabricks on Kubernetes(K8s)

Hi there,

For Parabricks .3.7, 3.8, we can setup parabricks.deb in Dockerfile, and then run the image on K8s.

But for Parbricks 4.0 installation, it is launched by docker container. In this case, we will face the docker-in-docker (dind) issue on K8s. Will you support the Debian Package Installation for v4.0, like v3.7, v3.8?

Best regards,

We do not plan to have Debian package for v4.0 but you should be able to run the new v4.0 docker container on K8s without issue now.

1 Like

After testing, I am able to run new v4.0 docker container on K8s.

i.e. it directly calls python3 to run tasks on a docker container.

# example
bash SRR7890827_germline_pipeline.sh
python3 /usr/bin/pbrun germline --ref /workspace/datasets/ref/Homo_sapiens_assembly38.fasta ...
python3 /usr/local/parabricks/run_pb.py fq2bam --ref ...
/usr/local/parabricks/binaries//bin/bwa mem /workspace/datasets/ref/Homo_sapiens_assembly38.fastq ...

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