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SBRun: tools to run CWL on Seven Bridges powered platforms

This package offers two command line tools sbpush and sbrun that push and run CWL tools on any Seven Bridges platform.

sbpush <cwl> <commit message> <profile> <user> <project> <app_id>
sbpush <cwl> <commit message>
sbpush <cwl>

sbrun <cwl>

sbpush uploads a CWL document to a SB platform. sbrun runs the CWL document.

If <profile> <user> <project> <app_id> are not supplied, sbrun looks in its cache for them as stored from a previous call. If a task has been previously run sbrun will clone the task and rerun it with the new version of the app. After pushing or running, the program will attempt to open a browser at the app or task page.

  • <cwl> - the path to the CWL file
  • <commit message> the commit message you want to appear for the revision
  • <profile> - profile name from your credentials file. For more details see below.
  • <user>, <project> - path to project on the platform
  • app_id - id of the app on the platform

Credentials file and profiles

If you use the SBG API you already have an API configuration file. If not, you should create one. It is located in ~/.sevenbridges/credentials.

Briefly, each section in the SBG configuration file (e.g. [cgc]) is a profile name and has two entries. The end-point and an authentication token, which you get from your developer tab on the platform.

[sbg-us]
api_endpoint = https://api.sbgenomics.com/v2
auth_token   = <dev token here>

[sbg-eu]
api_endpoint = https://eu-api.sbgenomics.com/v2
auth_token   = <dev token here>

[sbg-china]
api_endpoint = https://api.sevenbridges.cn/v2
auth_token   = <dev token here>

[cgc]
api_endpoint = https://cgc-api.sbgenomics.com/v2
auth_token   = <dev token here>

[cavatica]
api_endpoint = https://cavatica-api.sbgenomics.com/v2
auth_token   = <dev token here>

You can have several profiles on the same platform if, for example, you are an enterprise user and you belong to several divisions. Please refer to the API documentation for more detail.

Per app cached information

The <profile> <project> <app_id> information and the id of the most recent test task executed with the app is cached in a file under $XDG_DATA_HOME/sevenbridges/sb-run/scratch (which defaults to $HOME/.local/share/sevenbridges/sb-run/scratch)