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Galaxy Tool Linting and Tests for push and PR Weekly global Tool Linting and Tests

Galaxy tool repository template

This is a template repository to create IUC style repositories. It offers:

  • the same structure as the IUC repository
  • CI for pull requests and weekly CI for all tools
  • automatic Tool Shed deployment of any updated tools, if the CI passes

Some documentation of the structure and the use of the CI can be found in [here](TODO link to tutorial).

Setup

  • Adapt the repository owner from galaxyproject to the owner of your repository here, here and here. This is needed to forbid running the CI workflows in forks.
  • Change the links for the badges in this document here and here, i.e. chage the organisation and repository name in the links. Certainly you may want to add the other content of this document.
  • Add the API keys to the toolshed and testtoolshed as secrets with the name TTS_API_KEY and TS_API_KEY (for automated deployment).
  • Remove the example tool in tools/example

In order to use the /run-all-tool-tests slash command you need to add a secret PAT to your repo that allows the action to access you repository - see here. The slash command allows to run trigger weekly CI running using a given fork and branch of the Galaxy project, e.g. /run-all-tool-tests branch=release_21.05 fork=galaxyproject.

Also consider adding:

  • CONTRIBUTING.md
  • .github/CODEOWNERS
  • .github/PULL_REQUEST_TEMPLATE.md

Updates

Only the CI workflows may require updates from time to time. You can manually copy the latest version from this repository to your repository (not changing the repository owner as indicated in the setup section). We suggest to do this at least once a year, ideally with every Galaxy release.

Bug reports

Please report problems with the CI workflows here: IUC.