Monthly Archives: April 2012

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…

Draft post cull

Work and life are currently impacting the frequency of my blogging. I’m falling back on the old trick of clearing out draft posts and explaining briefly why they never saw the light of day.

1. How to launch a website (January 18, 2012)
Anyone can publish a website. Is this a good thing? In one sense yes, of course – empowerment and democratization of information are important. However, I’m increasingly of the opinion that scientific websites should meet some minimum standards and that those who create them have an appropriate level of programming competency. Having an idea is great but if it’s poorly-implemented, tools will break, whither and die, creating a Web of broken links and non-functional resources.

So the title of this post was supposed to be ironic and it went on to list a series of steps which described (wittily I hoped) how not to launch a website. Unfortunately, when I read over the post, it was not at all witty. In fact, it was just a thinly-veiled attack on a recently launched aggregator.

I think some of the points in the post do need to be made, but not in their current form and perhaps not by me.

2. Google Plus: what’s in it for the online scientist? (July 1, 2011)
I started to write this one when Google+ first launched. There were more than enough posts which reviewed its features so, as the title suggests, I was trying to come up with a different angle: how useful might G+ be for scientists?

In the end, I simply could not come up with anything interesting to say. I know that other scientists use G+ and find it very useful. I’m not one of them – in fact, I don’t use it at all. What’s more, I can’t even explain why. It’s not that I have strong feelings one way or the other about G+; for some reason, it just doesn’t register on my “must investigate” radar.

Still to come (hopefully)

1. Sequencing for relics from the Sanger era part 2: FASTQ manipulation and sequence quality
There are supposed to be 4 posts in my NGS series and this one looks at tools for manipulation and QC of FASTQ sequence files. My NGS self-education is a side-project and “real work” takes precedence just now, so no timeline promises for this one. Soon, I hope.

2. My day out at #osddmalaria
I’ve been meaning to write a summary of my day at the Open Source Drug Discovery Malaria meeting, back in February. Here’s a brief one: it was really interesting and I enjoyed it. More than that to follow at some point.