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Nersc has setup up gitlab repositories for our docker images. Among other things Gitlab incorporates a git based source code control system with continuous integration built in.

Step-by-step guide

Prerequisites:

  1.  Docker file created and pushed to JGI gitlab repository
  2.  The gitlab repository for your project has the NERSC runner enabled(Currently we need to request this to be done by the NERSC consultants)

Then:

  1. In your gitlab repo there is a file named .gitlab-ci.yml that will need to be edited
  2. Update the gitlab-ci.yml file to add the info for the shifter registry
  3. Barebones example listed below




  4. Commit the changes to gitlab
  5. The runner will then execute
  6. If it passes then it can then be pulled and run on Denovo
    1. To pull the image:

       

      shifterimg pull registry.services.nersc.gov/jgi/wgsim
       2017-05-15T15:58:26 Pulling Image: docker:registry.services.nersc.gov/jgi/wgsim, status: READY 


    2. And then run:

      shifter --image=registry.services.nersc.gov/jgi/wgsim wgsim <arguments>



 

 

 


 

Additional info on gitlab-ci.yml files

https://docs.gitlab.com/ce/ci/yaml/README.html

 

Related Jiras:

SEQQC-10883