Git for bioinformaticians at the Bioinformatics FOAM meeting

Last week, I attended the annual Computational and Simulation Sciences and eResearch Conference, hosted by CSIRO in Melbourne. The meeting includes a workshop that we call Bioinformatics FOAM (Focus On Analytical Methods). This year it was run over 2.5 days (up from the previous 1.5 by popular request); one day for internal CSIRO stuff and the rest open to external participants.

I had the pleasure of giving a brief presentation on the use of Git in bioinformatics. Nothing startling; aimed squarely at bioinformaticians who may have heard of version control in general and Git in particular but who are yet to employ either. I’m excited because for once I am free to share, resulting in my first upload to Slideshare in almost 4.5 years. You can view it here, or at the Australian Bioinformatics Network Slideshare, or in the embed below.

See the slides…

Redmine + Gitolite integration

I’m a big fan of both Redmine, the project management web application and Git, the distributed version control system.

Recently, I learned that it’s possible to integrate Git into Redmine so that git repositories for a project can be created via the Redmine web interface. This is done using plugins which connect Redmine with git hosting software: either gitosis or more recently, gitolite.

Unfortunately, this is a deeply-confusing process for novices like myself. There are multiple forks of the plugins, long threads in the Redmine forums that discuss various hacks/tweaks to make things work and no one authoritative source of documentation. After much experimentation, this is what worked for me. I can’t guarantee success for you.

Read the rest…