Duke-GCB/bespin-cli

Command line client for Bespin

bespin-cli

Command line client for Bespin

Example usage

Find job template tag

List workflows:

bespin workflow list

Output:

  Id  Name                     Job Template Tag
----  -----------------------  ------------------------------------------
   1  WES GATK4 Preprocessing  wes-gatk4-preprocessing/v1/b37-human-xgen

Create job template file

bespin job-template create wes-gatk4-preprocessing/v1/b37-human-xgen --outfile job1.yml

Output:

Wrote job file job1.yml.
Edit this file filling in TODO fields then run `bespin job create job1.yml` .

User edits job template file

Example job file:

fund_code: <String Value>
job_order:
  library: <String Value>
  read_pair:
    name: <String Value>
    read1_files:
    - class: File
      path: dds://<Project Name>/<File Path>
    read2_files:
    - class: File
      path: dds://<Project Name>/<File Path>
name: <String Value>
tag: wes-gatk4-preprocessing/v1/b37-human-xgen

User will replace all TODO fields with actual values.

Create job using job template file

bespin job create job1.yml

Output:

Created job 1

Check Status of the job

bespin job list

Output:

  Id  Name                      State    Step    Last Updated                   Elapsed Hours  Workflow Version Tag
----  ------------------------  -------  ------  ---------------------------  ---------------  ---------------------------
   1  My                        A                2018-11-15T17:02:44.224348Z                0  wes-gatk4-preprocessing/v1   

Start running the job

Start running a job

bespin job start 1

Create and start a job in one step

bespin job run job1.yml