Re: Debian Med Bioinformatics Sprint in Lübeck : post-install

2011-02-03 Thread Tim Booth
Some answers on BLAST+ and T-Coffee... > > 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. > > Did you actually found out what BLAST+ is (I remember you were wonde

Re: Debian Med Bioinformatics Sprint in Lübeck : post-install

2011-02-03 Thread Andreas Tille
Hi Olivier, On Thu, Feb 03, 2011 at 09:29:19AM +0100, Olivier Sallou wrote: > Just a hint on Blast+ > > This is a rewrite of Blast2 with performance improvements and supposed > eaiser to use. > But binaries and options were changed. There is a small fdscription we > made herte: http://drmotif

Re: Debian Med Bioinformatics Sprint in Lübeck : post-install

2011-02-03 Thread Olivier Sallou
Regarding biomaj, I have created a get-orig-source to download source code and rearrange it to create the debian structure, to be used for packaging. We have an issue with our forge that is being fixed, so it cannot be tested for the moment, but it should be ready in the next few days. On our

Re: Debian Med Bioinformatics Sprint in Lübeck : post-install

2011-02-03 Thread Olivier Sallou
Just a hint on Blast+ This is a rewrite of Blast2 with performance improvements and supposed eaiser to use. But binaries and options were changed. There is a small fdscription we made herte: http://drmotifs.genouest.org/2011/02/new-blast-web-form/ Le 2/2/11 10:08 PM, Andreas Tille a écrit :

Re: Debian Med Bioinformatics Sprint in Lübeck : post-install

2011-02-02 Thread Andreas Tille
On Wed, Feb 02, 2011 at 06:19:57PM +, Tim Booth wrote: > 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. Ahh, hmm,

Re: Debian Med Bioinformatics Sprint in Lübeck : post-install

2011-02-02 Thread Tim Booth
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 point

Re: Debian Med Bioinformatics Sprint in Lübeck : post-install

2011-02-02 Thread Andreas Tille
Meta-remark: I removed those e-mail addresses where I know people are reading Debian Med list (specifically lea...@debian.org who was interested in the general resume but not in detailed discussion). I would be happy if we could move the discussion to debian-med@lists.debian.org without the long C

Re: Debian Med Bioinformatics Sprint in Lübeck : post-install

2011-02-02 Thread Andreas Tille
On Wed, Feb 02, 2011 at 10:26:27AM +0100, Pjotr Prins wrote: > I also enjoyed the conf. One result is a further collaboration on > EMBOSS bindings to Perl, Python, Ruby and the JVM. Fine. > > Cool - but what is rq? I can't find it in SVN nor on our tasks page. > > Brilliant tool for paralleliz

Re: Debian Med Bioinformatics Sprint in Lübeck : post-install

2011-02-02 Thread Pjotr Prins
I also enjoyed the conf. One result is a further collaboration on EMBOSS bindings to Perl, Python, Ruby and the JVM. > Cool - but what is rq? I can't find it in SVN nor on our tasks page. Brilliant tool for parallelized running of programs. Like Gridengine, or Torque, but *much* simpler to set u

Re: Debian Med Bioinformatics Sprint in Lübeck : post-install

2011-02-02 Thread Andreas Tille
Hi Steffen, I took the freedom to publish your (actually not that private) mail to the Debian Med mailing list because on one hand it is interesting in general for the list on the other hand we are responsible to give a report to the Debian community which was supporting our sprint. On Wed, Feb 0

[Debian Med] Bioinformatics Sprint

2011-01-07 Thread Steffen Möller
Dear all, Many of you are aware of the many constructive roles that computers have in preclinical research. And in the post-genome area, free access to those data goes closely together with free access to tools to access those data. Debian, Ubuntu and Open Source technologies at large are hence ex