Using ElasticBLAST with command line parameters¶

ElasticBLAST supports selected command line parameters illustrated by this tutorial. This tutorial accomplishes the same goals as those provided in the quickstart, and assumes the same conventions.

The primary difference in ElasticBLAST parameters between cloud providers is that for AWS, the s3:// prefix in the results is leveraged to determine that the Cloud Service Provider is AWS and the us-east-1 AWS region is used by default. The AWS region can be overriden with the --aws-region parameter.

In contrast, GCP requires the explicit specification of the GCP project.

Search submission¶

Use the appropriate command based on your cloud service provider to submit an ElasticBLAST search.

BLAST+ parameters are specified after a -- at the end of the command.

Please note that the the labels configuration parameter is not supported by the command line interface.

AWS¶

elastic-blast submit \
    --program blastp \
    --db refseq_protein \
    --query s3://elasticblast-test/queries/BDQA01.1.fsa_aa \
    --results s3://elasticblast-YOURNAME/results/BDQA \
    --num-nodes 2 \
    -- -task blastp-fast -evalue 0.01 -outfmt "7 std sskingdoms ssciname"

GCP¶

elastic-blast submit \
    --gcp-project ${YOUR_GCP_PROJECT_ID} \
    --program blastp \
    --db refseq_protein \
    --query gs://elastic-blast-samples/queries/protein/BDQA01.1.fsa_aa \
    --results gs://elasticblast-${USER}/results/BDQA \
    --num-nodes 2 \
    -- -task blastp-fast -evalue 0.01 -outfmt "7 std sskingdoms ssciname"

Checking search status¶

Use the appropriate command based on your cloud service provider to check the status of an ElasticBLAST search.

AWS¶

 elastic-blast status --results ${YOUR_RESULTS_BUCKET}

GCP¶

 elastic-blast status --results ${YOUR_RESULTS_BUCKET} \
    --gcp-project ${YOUR_GCP_PROJECT_ID}

Deleting cloud resources¶

This step is required if the Auto-shutdown feature is not enabled.

Use the appropriate command based on your cloud service provider to delete an ElasticBLAST search.

AWS¶

 elastic-blast delete --results ${YOUR_RESULTS_BUCKET}

GCP¶

 elastic-blast delete --results ${YOUR_RESULTS_BUCKET} \
    --gcp-project ${YOUR_GCP_PROJECT_ID}