# Running CWL in Jenkins

#### Running the Script

1. Log into Jenkins:
   * &#x20;[http://voyager.mskcc.org:8080/](http://voyager.mskcc.org:8080/l)
   * 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.\
   ![](https://548551270-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2F-MXY9KcVjrKoEWe0OQVs%2Fuploads%2FO2zv2Z1JeWspY57xuWIm%2Fimage.png?alt=media\&token=749774cf-1975-47ae-aaf0-8d133e4e190a)
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.

{% hint style="info" %}
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&#x20;

ex:<mark style="color:red;">/</mark>juno/work/ci/dpankey/test\_inputs/ALN\_REQ-alignment.json
{% endhint %}

### 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.&#x20;
   * 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&#x20;

     <figure><img src="https://548551270-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2F-MXY9KcVjrKoEWe0OQVs%2Fuploads%2Fd3vi8kn41EG4cbIVekwx%2Fimage.png?alt=media&#x26;token=7ac4596d-ba30-4f88-9e1e-ac0fbfcb2382" alt=""><figcaption></figcaption></figure>
2. Once you click on the build number. Click Console Output in the sidebar menu and the console output is displayed

#### Output directory   &#x20;

&#x20;The ouput folder and toil log can be found in the following directory: `/work/ci/jenkins/parameterized-cwl-script/{build-number}/`
