JAWS TEAMS

“JAWS Teams” is a feature designed to simplify user management and enhance the efficiency of output file sharing and delivery within your teams.

Commands

List All Available Teams

jaws teams list
  [
      "gt-ga",
      "nmdc",
      "dsi-ii",
      "bionano",
      "sc-mcr",
      "dsi-syseng",
      "ornl",
      "workshop",
      "plant_ha",
      "kbase",
      "mycocosm",
      "plantcompgen",
      "gaa",
      "gt-seqtech",
      "funcgen",
      "sc-mds",
      "gt-usa",
      "micro-scale",
      "rqc",
      "dsi-aa",
      "gt-syn",
      "phytzm"
  ]

List Teams You Belong To

jaws teams my-teams
[
    "dsi-aa"
]

List Team Members

jaws teams members dsi-aa
[
    "dcassol",
...
]

Get a Team’s Designated Output Path

jaws teams get-site-path dsi-aa dori
"/clusterfs/jgi/scratch/dsi/aa/jaws/dsi-aa/output"

Manage Team Settings and Memberships

Responsibilities of the Team’s Owner

Team’s owner has power and responsibilities, including managing the team’s output path for each site, adding and deleting users from the team.

Commands for Team Management

The following commands allow the team owner to perform these tasks:

# Set the site-specific output path for the team
jaws teams set-site-path <TEAM_ID> <SITE_ID> <PATH>

# Add a new user to the team
jaws teams add-user <TEAM_ID> <USER_ID>

# Remove a user from the team
jaws teams remove-user <TEAM_ID> <USER_ID>

Setting Correct Permissions

When setting a new path, the team’s owner must set the correct permissions to ensure access for JAWS to read and write to the new location.

NERSC - Perlmutter

For paths located on NERSC, set the permissions using the following command:

setfacl -m d:g:"genome":rwx "<PATH>"

NERSC - NMDC

For paths located on NERSC for the NMDC project, set the permissions using the following command:

setfacl -m d:g:"nmdc":rwx "<PATH>"

NERSC - KBase

For paths located on NERSC for the KBase project, set the permissions using the following command:

setfacl -m d:g:"kbase":rwx "<PATH>"

How to use Jaws Teams?

When submitting a new run, you can use --team flag. The outputs for this run will be transferred to the team’s path.

jaws submit align_final.wdl inputs.json dori --team=dsi-aa

As an easy alternative, you can set the default_team at your jaws.conf file:

vi ~/jaws.conf

[USER]
token = <TOKEN>
default_team = dsi-aa

Important: Do not use quotes for the team’s name.

The Jaws Team’s feature will transfer the final workflow outputs from cromwell-execution to the path defined for your team.

How do I find the output data?

jaws status <RUN_ID> will provide the path to final path. Please check output_dir.

Then, you can find the expected file tree structure:

/<TEAM PATH>/<USER_ID>/<RUN_ID>/<Cromwell_ID>

JAWS will copy the following in case of a successful run:

Workflow outputs;
Supplementary files:
- *.wdl;
- *.json;
- errors.json;
- metadata.json;
- output_manifest.json;
- outputs.json;
- summary.json;
- tasks.json

In case of a FAILED run, JAWS will skip the transfer of the output files. However, it’s possible to ‘force’ the download, by using jaws download <RUN_ID>. In this case, JAWS will copy the following:

Workflow outputs;
Supplementary files;
Failed tasks’ cromwell-execution folder only.

As we transition to copying the output files, we are deprecating out the jaws get command. To ensure backward compatibility, this command will remain functional for a few more months, serving solely to copy the final workflow outputs. However, please note that we plan to discontinue this command entirely in upcoming cycles.