cloud resources - NCBI-Codeathons/psss-team4 GitHub Wiki

GCP

Project: codeathon-psss-2021

Data

Bucket: gs://psss-team4

Compute

VM

VM Instance: psss-team4

  • gcloud compute ssh psss-team4 --zone us-east4-c --ssh-flag=-A

To copy from your localhost to that instance:

  • gcloud compute scp ${LOCAL_FILE} psss-team4: --zone us-east4-c

To copy from the instance to your localhost:

  • gcloud compute scp psss-team4:${PATH_TO_YOUR_FILE} . --zone us-east4-c

Software installed:

  • elastic-blast 0.1.9
  • BLAST+ 2.12.0
  • SRA toolkit 2.11.1
  • /usr/local/bin/psearch_gcp.sh

Cloud Function

get-fasta

Usage examples:

  • gcloud functions call get_fasta --data='{"run_accession": "ERR164407"}' (for testing only)
  • curl -X POST "https://us-east4-codeathon-psss-2021.cloudfunctions.net/get_fasta" -H "Content-Type:application/json" -d '{"run_accession": "ERR164407", "upload_bucket": "psss-team4", "upload_prefix": "victorlin-test-fasta/"}'