How to update your software tool in PhenoMeNal

Updating software tools

If you want to add a new tool to PhenoMeNal, check in the guide "How to make your software tool available through PhenoMeNal".

Updating software tools requires checking in a few different places to ensure all the components required to run the software tools in PhenoMeNal Galaxy work together.

• Update your Galaxy XML definition
  • bump version if you change anything here
  • add short release note in the NEWS section of your Galaxy XML
• Update your software tool container
  • bump version if you change anything here (version of underlying software + version of Dockerfile). Please follow versioning conventions available on the container release process guide.
• Build your software tool container in Jenkins
  • container should be built automatically once changes are pushed to the container GitHub project
• Update container-k8s-galaxy-runtime with your updated Galaxy XML and the container image tag from Jenkins)
  • clone repository (develop branch)
  • create a new feature branch for your changes (e.g. feature/my_tool_updates)
  • if you changed your Galaxy XML, place it into the correct location in container-galaxy-k8s-runtime/tools/phenomenal/
  • container-galaxy-k8s-runtime/config/phenomenal_tools2container.yaml needs the new version tag from the Jenkins build (or "latest")
  • Important: Test your changes in Galaxy. Please refer to "QuickStart Installation for Local PhenoMeNal Workflow" to setup a local testing environment via minikube.
  • perform Pull Request to integrate your changes in the official PhenoMeNal develop branch of container-galaxy-k8s-runtime
  • make sure you request reviewers on your Pull Request!

Note 1: This reference manual only tells you how to make your updated tool available in the develop branch used for testing and development. To freeze your tool changes and make them available in a release you still need to make your changes available in the stable branch. Please see Tool container release process.

Note 2: For contributing directly to the release, please also check the Tool spreadsheet for releases.

(TODO: Finish writing this)