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Submitting patches to Jalview

The easiest route for creating a patch is:

  1. Create an issue for your patch over at
  2. Decide which build you'd like to patch. If you need a patch for a version currently released, then its code lives in a branch called Release_W_X_Y_Branch.
  3. Clone the Jalview GIT repo, and create a new branch to create your patch off the branch for the version you want to patch. If you call your branch patch/JAL-QQQQ that'll help us track merges associated with that issue.
  4. If you are fixing bugs, etc, create and commit a new test under test/' to demonstrate the bug before you start fixing it.
  5. Hack away....
  6. Commit everything to your patch/JAL-QQQQ branch.
  7. Do a git pull origin to update your local copy of Jalview's release branches. Try to merge in changes, or even rebase your local patch branch if your comfy with that.

Sharing your patch

If you aren't a Jalview developer, you don't have commit rights. You can create a patch using git by:

git diff Release_W_X_Y_Branch > JAL-QQQQ.patch

Then upload the patch as an attachment on and poke one of the developers to take a look (if a developer is already assigned, they'll get an email when you create an attachment or comment on the issue, so poking has already happened).

If you have commit rights, then you're also able to create branches. If your patch is substantial, then you might want to push your branch to the server and ask people to test (mailing list, put a comment on the JIRA issue, etc). Otherwise, do a trial merge to the base branch, and if everything checks out, consider porting the patch to the develop and next-release branches.