Re: Debian Med Bioinformatics Sprint in Lübeck : post-install
Hi All,
I'll echo Steffen and Andreas' comments that I really enjoyed the
meeting and the amount of focused work and interaction going on was
fantastic. I'll make sure to finish my "homework" from the meeting but
right now I'm back to trying to sort out all sorts of things at work.
My main points from the meeting:
* Meeting, learning, getting inspiration
* Updating T-Coffe with Paolo and reviewing package dependencies
* Packaging TMalign and Mothur with much help from Andreas
* Starting to add to and update the Deb Med wiki pages
* Clarifying relationship of Deb-Med and Bio-Linux
* Clarifying how to combine Ubuntu LTS development and SVN
contributions
> Andreas:
> I would be happy if we could move the discussion to
> debian-med@lists.debian.org without the long CC list if I could assume
> that nobody, who is really interested in this topic will miss the
> information. So in my next mail I'll probably strip the CC list and
> there is always the archive of the list in case somebody is interested
> but is afraid of the list.
I generally have an aversion to mailing list servers that create a
public mail archive with e-mail addresses unobfuscated, but as I see the
damage is now done and my address is on there for all to spam I may as
well join.
> Steffen:
> > * Tim is happy about using the Debian Med repository for more than he did before and the presumed Debian vs Ubuntu packaging
> > conflict was nullified, at least Andreas and I have, with help from Will, understood BioLinux as a better non-free for all those
> > packages that Debian would not want to redistribute as they are. Conversely, BioLinux is likely to present itself more as an
> > extension of Debian Med. They have a repository for amd64 that we can use already today.
Absolutely.
Andreas:
> I'm really keen on enhancing the cooperation with Bio-Linux as far as
> possible.
Seconded. Hopefully there will still be a NERC-funded Bio-Linux project
in 6 months. I didn't talk much (or at all) in the meeting about the
JCVI CloudBioLinux project (Steffen was at the
sprint/aka:codefest/aka:hackathon for that just before BOSC) but there
is also some progress on that and I'll do my best to ensure that all
relevant news is transmitted from the CBL lists to Deb-Med and
vice-versa, especially if I spot any signs of redundant work or events
that might be of interest.
I was also asked by Steffen to edit the Wiki page to clarify the
relationship with Bio-Linux and also to add some information about
learning to package - ie. links to helpful resources. The page at the
moment rather assumes that you already know how to package. It also
outlines a development process using SVN-buildpackage that nobody
actually seems to follow in real life.
Also the page needs to say something to non-developers who come looking
for software. It's not immediately clear to a newcomer what exactly
Debian Med is doing and why there are no direct package downloads on the
site. (The phrase "Pure Blend" does not mean much to the average user).
Maybe a short FAQ is appropriate?
Steffen:
> > * T-Coffee packaging was updated by Tim, Paolo and ... Andreas? Having Paolo from the upstream group as a maintainer would be
> > great, I am just somewhat uncertain about the degree of co-maintainership that was reached during that meeting.
Andreas:
> I'm not aware that I did something about T-Coffee (even if I admit I
> touched a lot of stuff and might have mixed up things). The only thing
> what I did is working on TMalign which is also soon to be uploaded after
> I've got a very quick and helpful response from upstream (more in a
> separate mail).
During the meeting I was editing the T-Coffee package on my laptop as I
had a head start over Paolo in terms of software setup and understanding
of package building tools. Our main achievement was to review and
update all dependencies (T-Coffee has many). TMalign along with BLAST+
enables a key mode of operation in T-Coffee but currently the BLAST+ bit
only works with our bio-linux-blast+ package. I'm continuing to work on
this.
Apart from that we compiled the latest upstream (only on Ubuntu Lucid -
someone needs to try it on Sid!) and also did a bit of tidying with help
from Andreas.
Paolo should still be the maintainer of this package from now on, unless
we scared him off ;-) As I now have a lot more confidence about my
understanding of packaging I'll try to help and encourage him (and
others) on the list.
Andreas:
> I've actually got some packages close to upload. The first of them
> (mothur) was uploaded just now to new.
Excellent news on Mothur after it sat in the SVN for so long due to
license ambiguity. This is a very important package to me so maybe a
logical one for me to take on as maintainer once it goes in?
Steffen:
> > * Please send in your suggestions for the next meeting
I was pondering on the train home if there was anywhere round here that
would be suitable. Oxford is expensive and transport is not the best
(you have to fly to London Heathrow and get a bus) but the OeRC might
well offer to host it. I definitely liked having the hacking right in
the hotel though so maybe we should stick with out-of-season coastal
towns that have rail links and find a similar hotel again. Southend?
Bognor Regis? Weston-super-Mare? Walton on the Naze? What do my
fellow Brits think?
Cheers,
TIM
--
Tim Booth <tbooth@ceh.ac.uk>
NERC Environmental Bioinformatics Centre
Centre for Ecology and Hydrology
Maclean Bldg, Benson Lane
Crowmarsh Gifford
Wallingford, England
OX10 8BB
+44 1491 69 2705
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