helios edited this page Sep 12, 2010 · 13 revisions
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Welcome to the git home for the bioruby project. Here’s where all development of the project goes on.

How does collaboration work?

To get a feel for how collaboration using git works, have a look at this blog post by DrNic.

This screencast is another must-see. Apart from other things, it explains different ways of collaborating (fast-forward to 48min14sec): the central repository model, the dictator and lieutenants model and the integration manager model. Bioruby uses something like this integration manager model, but with 3 or 4 integration managers instead of just one. Also, this screencast has a good explanation of how you can manage your local bioruby clone and play with different branches (production, development, feature branches, …). You’ll have to fast-forward to 38min54sec for that.

Finally, see here for the implementation for bioruby.

How to get your own copy

There are several ways of getting a copy of bioruby.

  • Install the gem:
    gem sources -a http://gems.github.com (you only have to do this once)
    gem install bio
  • Create a local clone
    git clone http://github.com/bioruby/bioruby.git
  • Create a fork on github: Click the “fork” button.

How to get to a remote branch

There might be other branches than just master (e.g. biohackathon2008). To make that locally available, use

git checkout —track -b biohackathon2008 origin/biohackathon2008


See the bioruby homepage.

Additional documentation

Getting in touch

Of course there is the mailing list on the bioruby homepage. Some of us also hang out on the FriendFeed Ruby for Bioinformatics room.


  • The bioruby homepage is at http://bioruby.open-bio.org
  • Bug reports and feature requests are to go here