Saving BLAST Results

This example BLAST workflow can save the generated output file results/blastp.out to a destination of your choice. This section walks through how you can save the output file to S3.

In order to write the output file to an S3 bucket, you may need access to a Fuzzball S3 secret. Please see the Fuzzball secrets guide for instructions on how to set one up.

You can set up your workflow to save an output file to S3 through the GUI or by editing the Fuzzfile.

select

Please select either the GUI or Edit Fuzzfile tab to see the appropriate instructions on how to save output file results/blastp.out to S3.

GUI

After opening the workflow in the Fuzzball GUI, you can select any job in the workflow editor and navigate to the volumes tab.

Volumes tab selected

You can edit the settings of blast-volume by clicking on it. You can specify a destination for output file results/blastp.out by clicking “Add Egress” which will bring up a pop-up.

BLAST Volume selected

First, specify the source and destination location of the result file. Next, you can select the secret which will be used to write your output file to the destination using the drop down. Optionally you can specify a timeout and retry attempts. The screenshot below saves output file results/blastp.out to S3 URI s3://my-bucket/my-dir/results/blastp.out. Fuzzball user secret my-s3-bucket-secret is used to write to S3 bucket s3://my-bucket/. When you are done editing your egress configuration, you can click “OK”.

BLAST output file egress configured

When you are done editing your volume settings, you can click the “Save” button.

BLAST volume settings ready to save

Edit Fuzzfile

Editting the Fuzzfile to save output file results/blastp.out can be done in the GUI after opening the Fuzzfile by clicking the ellipses (...) menu in the lower right and select “Edit YAML” or simply press e on your keyboard. An editor with the workflow’s Fuzzfile will appear shown in the screenshot below. If you are using the CLI, the Fuzzfile can be edited in a text editor of your choice.

Editor with BLAST Fuzzfile

The Fuzzfile in the previous section uses ephemeral volume blast-volume with an egress block commented out.

volumes:
  blast-volume:
    name: blast-volume
    reference: volume://user/ephemeral
    # egress:
    #   - source:
    #       uri: file://results/blastp.out
    #     destination:
    #       uri:
    #       secret:

To save output results/blastp.out to S3 by editting the Fuzzfile, you can uncomment the egress section, specify a destination with an S3 URI and a Fuzzball secret. The volumes block below writes workflow output file results/blastp.out to destination S3 URI s3://my-bucket/my-dir/results/blastp.out. The credentials used to egress this file is Fuzzball user secret secret://user/my-s3-bucket-secret.

volumes:
  blast-volume:
    name: blast-volume
    reference: volume://user/ephemeral
    egress:
      - source:
          uri: file://results/blastp.out
        destination:
          uri: s3://my-bucket/my-dir/results/blastp.out
          secret: secret://user/my-s3-bucket-secret