9e75f44f1a
Source-only snapshot of the cluster branch for WES execution. Large reference files (HPA/MANE/ensemble FASTA, model weights, ~597 MB) are omitted: they are baked into the container images at build time and mounted from the dreamdock-data PVC at runtime, and exceed the Gitea request size limit. Pipeline entry point is main.nf, which orchestrates the biotransformer, conplex and tissue modules as a single workflow. Ligand inputs are read from the eureka workspace; protein_zarr and chembl_db come from the dreamdock-data PVC.
779 B
779 B
access the current workspace
kubectl exec -it -n bioinformatics $(kubectl get pod -l app=digital-trials-nextflow -n bioinformatics | grep Run | awk '{ print $1 }') -- bash nextflow run main.nf -profile k8s
DEPRECATE: cleanup error pods in bioinformatics
kubectl get pod -n bioinformatics | grep -E "Pending|Error" | awk '{print $1}' | xargs -P 10 -I {} kubectl delete pod -n bioinformatics {}
sync data (/data/bugra/similarity-search/utility/vec_db/nf_fingerptint) from node to workspace
kubectl delete -f k8s/job-copy-node-to-pvc.yaml; kubectl apply -f k8s/job-copy-node-to-pvc.yaml
run the actual nextflow jobs
kubectl apply -f k8s/job-nextflow-digital-trials.yaml
[WARNING] destroy the curent nextflow job
kubectl delete -f k8s/job-nextflow-digital-trials.yaml