Running CWL in Jenkins

Jenkins will run a toil script that loads environment variables, and runs argos CWL based on parameters provided by the user.

Running the Script

1. Log into Jenkins:

   • http://voyager.mskcc.org:8080/

   • username and password can be found/work/ci/jenkins_secrets.txt

2. Once logged in click 'parameterized-cwl-script'. This will navigate you to the parameterized Jenkins job.

3. On the left hand side select 'Build with Parameters'. Default parameters will load in the text box and can be modified. The required parameters are:

   • GIT_CLONE: The CWL Github repository

   • GIT_CHECKOUT: The branch (or tag) the user is working on

   • CWL_PATH: The path to CWL within the github repository

   • INPUT_JSON: The path to input.json or yaml file. This path can be within the github repository or a directory in juno.

4. Once parameters are entered click on the 'Build'. This will run the parameterized script.

If the CWL path or Input JSON path is within the github repo do not include a forward slash at the begining of the path.

ex: argos-cwl/test/inputs.yaml

Include forward slash at begining of path if the path is outside of git repo

ex:/juno/work/ci/dpankey/test_inputs/ALN_REQ-alignment.json

Confirm script is running

While the build is running, you can view a detailed log of the build from the console output.

1. Hover over the Build History table in the sidebar.

   • Clicking the up arrow will confirm you are clicking on the most recent build

   • Clicking on the build number will take you to the console output

   • Hovering over the circle next to the build number will show you the progress of the run

     
2. Once you click on the build number. Click Console Output in the sidebar menu and the console output is displayed

Output directory

The ouput folder and toil log can be found in the following directory: /work/ci/jenkins/parameterized-cwl-script/{build-number}/