Biowulf High Performance Computing at the NIH
Seven Bridges CLI on Biowulf

The Seven Bridges CLI, or SB CLI, lets users access a Seven Bridges platform using the API from the command line. The interface allows users to configure an API endpoint along with a corresponding authentication token. Use these credentials users can access a variety of information like their projects, tasks, and files, which can be downloaded or uploaded.

Important Notes

Interactive job
Interactive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs.

Allocate an interactive session and run the program. The module is also available on Helix.
Sample session (user input in bold):

[user@biowulf]$ sinteractive
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load sb_cli
[+] Loading sb_cli 0.18.4  ...

[user@cn3144 ~]$ sb configure
Seven Bridges API endpoint:
Seven Bridges authorization token: ****************
Seven Bridges advance access (true/false): false

[user@cn3144 ~]$ sb --output table files list \
                    --project username/test-project \
                    --origin 1c46ecb3-772d-46b4-88db-6b423e75e811
|            ID            |             Name              |
| 61d5f311e722267a17c521f6 | G20502.22Rv1.2_fastqc.b64html |
| 61d5f2f9e722267a17c521b3 |     |

[user@cn3144 ~]$ sb download --file 61d5f311e722267a17c521f6
Downloading file `G20502.22Rv1.2_fastqc.b64html` with ID `61d5f311e722267a17c521f6`.
  479.40 KiB / 479.40 KiB ┃▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓┃100.00% 1.70 MiB/s 0s
'success'   '61d5f311e722267a17c521f6'      'G20502.22Rv1.2_fastqc.b64html` '490910'

[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$