[Date Prev][Date Next] [Thread Prev][Thread Next] [Date Index] [Thread Index]

Re: My report from Debian Med sprint 1.+2. February 2014 in Stonehaven

Dear all,

Below is my report from the Debian Med sprint in Stonehaven

On the first evening (31 January) I gave a short presentation,
'Bioinformatics education: the 4273pi project', about our educational work
using low-cost Raspberry Pi computers
(http://eggg.st-andrews.ac.uk/4273pi) and how it might fit with Debian-Med
in the future.

We used a Raspberry Pi, running 4273pi, to give my presentation and
Detlev's first presentation.

On the second day, I attended Andreas' excellent tutorial on how to create

Before the event, I had thought our phylogeny program LVB might be a
useful first thing to package (http://eggg.st-andrews.ac.uk/lvb). However,
the licence would bar it from the main repository. We will address that
upstream first. We planned to do this anyway, but it will take some time.

Working on Linaro (Ubuntu) for the ARM-based Cotton Candy
(http://www.fxitech.com), I decided to package Nw-align. At an early stage
I found the software does not work, at least on this platform. I did not
try other platforms. I abandoned this packaging effort.

I turned my attention to Ngila, whose packaging remains work-in-progress.
I will complete this within the next couple of weeks.

I realised it will be technically fairly easy to package 4273pi
Bioinformatics for Biologists for Debian-Med when we are ready. First,
there are matters we would like to work on (upstream), most of which are
not specific to Debian-Med. This is good news.

One excuse for my gentle pace was, excellent and helpful conversations
with other participants. Many of the presentations were timely for me. We
are part-way through setting up a new cluster
(http://bioinformatics.st-andrews.ac.uk/cluster). My university is also
starting to think about creating an institution-wide networked file store
for research data. For doing the latter effectively, I can see analogies
with what Luca has achieved. Distributed/peer-to-peer are now being
considered along with other options.

I enjoyed the whole event. Among other things, I got from it exactly what
I wanted to know - i.e. how to make Debian-Med packages. This information
is online, but anything of this complexity is rather daunting without a
tutorial in person. I will still get things wrong, but there's plenty of
help available.

Many thanks to the organisers, presenters and participants.

Best wishes,


Daniel Barker
The University of St Andrews is a charity registered in Scotland :
No SC013532

Reply to: