July 8, 2015

BOSC Codefest 2015

Robin Andeer

Day 1

After a less than ideal breakfast, me and Johan Dahlberg headed to Trinity College for the first day of the Codefest hackathon. We got there well in time to meet with Brad Chapman who organizes the event.

The day started out with introductions to give people an idea of who is there and what everyone is keen on hacking on for the next couple of days. Three groups take form: a very large Common Workflow Language (CWL) group, an R group working on a web interface, and a BioPython group resolving outstanding issues.

I’m joining one small corner of the CWL group. First on the agenda is an improvised intro to the project. We don’t start out with any clear goal. After trying to install and run some simple examples we kind of slip into figuring out how to make the reference implementation run on Mac using the Docker integration. By the end of the day we have a fix in an open pull request smiley When the changes are merged we will be official contributors of CWL.

Day 2

Continued progress on the boot2docker support for CWL. We lost Roman Valls but was able to wire up the pull request so it now passes “all” the conformance tests running on Mac OSX.

Also had a chance to talk more to the R-people doing interesting work on a web app to display coverage data for gene panels. A little later I was introduced to one of the Sambamba authors (Pjotr Prins) who is a very nice guy and invested in open source and building tools according to the UNIX philosophy. I was encouraged to keep sending feature requests to Artem, the genius behind the Samtools-killer, to keep him busy smile

Had a bit of a down time towards the end of the day where I didn’t really feel I had either the energy or the time to really push out some much needed hacking on Chanjo.

That’s my first hackathon experience. It’s was just as easy to apporach people about interesting projects. I think it would’ve been even more productive if the projects were more well defined before the start of the Codefest but I’m still quite happy and intrigued to join more of these events.