sbpack 2020.6.1

Command line tool to upload CWL documents to SB powered platforms.

sbpack

Upload CWL apps to any Seven Bridges powered platform. Resolves linked processes, schemadefs and $includes and $imports.

Installation

(It is good practice to install Python programs in a virtual environment. pipx is a very effective tool for installing command line Python tools in isolated environments)

sbpack needs Python 3.6 or later

pip3 install pipx  # in case you don't have pipx
pipx ensurepath # ensures CLI application directory is on your $PATH
pipx install git+https://github.com/kaushik-work/sbpack.git
# use pipx upgrade ... if upgrading an existing install

Usage

Usage
   sbpack <profile> <id> <cwl>

where:
  <profile> refers to a SB platform profile as set in the SB API credentials file.
  <id> takes the form {user}/{project}/{app_id} which installs (or updates) 
       "app_id" located in "project" of "user".
  <cwl> is the path to the main CWL file to be uploaded. This can be a remote file.

Uploading workflows defined remotely

sbpack handles local paths and remote URLs in a principled manner. This means that sbpack will handle packing and uploading a local workflow that links to a remote workflow which itself has linked workflows. It will therefore also handle packing a fully remote workflow.

For example, to pack and upload the workflow located at https://github.com/Duke-GCB/GGR-cwl/blob/master/v1.0/ATAC-seq_pipeline/pipeline-se.cwl go to the raw button and use that URL, like:

sbpack sbg kghosesbg/sbpla-31744/ATAC-seq-pipeline-se https://raw.githubusercontent.com/Duke-GCB/GGR-cwl/master/v1.0/ATAC-seq_pipeline/pipeline-se.cwl

Local packing

Usage
    cwlpack <cwl> > packed.cwl

The cwlpack utility allows you to pack a workflow and print it out on stdout instead of uploading it to a SB 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. (Documentation)

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>

[nhlbi]
api_endpoint = https://api.sb.biodatacatalyst.nhlbi.nih.gov/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.