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GitHub pointers for GO Consortium members
This page is a placeholder for documentation on github for members of the GO Consortium. Depending on your role, a different level of knowledge is required.
Everyone in the GOC should sign up for an account. Join here.
Here are some useful repositories (call these 'repos' if you want to sound like a git guru)
- https://github.com/geneontology/go-site - where we track issues relating to the Drupal site and metadata
- https://github.com/geneontology/amigo - AmiGO
- https://github.com/geneontology/noctua
- GO Ontology (to be moved)
- PAINT (to be moved)
- touchup (to be moved from Suzi's repo to the geneontology organization)
For any 'repo', the part you care about most will be the link that says "issues" on the right hand side of the screen.
Currently the ontology lives in GO production SVN and the tracker lives on sourceforge. If we move to GH, the Ontology Group should be able to transfer all current SVN operations onto the equivalent git operations. This is relatively straightforward; one thing to bear in mind is that an extra step is required to 'push' your changes to github.
Your general routine will be:
git pull ## just like "svn update"
[work on ontology]
git commit gene_ontology_write.obo ## just like "svn commit", but local
git push origin master ## synchronize local commits with github. No equivalent in SVN
Additionally, there are some nice features the ontology group will enjoy. For example, you can reference any ticket in a commit message by preceding with a hash, e.g. #123 for issue 123. This will link the commit message into the tracker conversation. Tickets can also be closed within a commit message, e.g. fixes #123.
Some repos of interest:
- https://github.com/geneontology/termgenie - for the TermGenie software, not actual TG requests!
- Cell Ontology (to be moved)
- https://github.com/owlcollab/owltools
- https://github.com/protegeproject/protege/
Most members of GOC who are involved in developing or deploying software should be familiar with git, github and features such as forks, branches, pull requests. Later on we will document best practices here. Of course, the overriding one is "commit early, commit often"
Please add your favorite guides here: