On 04/01/2011 07:52 AM, George Marselis wrote: > Oh, man, ideas galore... i was in the #bioinformatics channel on > freenode the other day. One of my users had asked me to install 20-odd > tools... i was frustrated that a lot of tools do not come with a > configure script or the code is just $h17 and does not compile unless > you have the astronomical luck of having the same gpfs path... > Such tasks are fine when you do them for your own interest in the tool ... > I was also frustrated by the -apparent- lack of a list of all the > bioinformatics application. It did not have to be complete, it just > has to be complete enough, so maybe I can start on that memory > profiling framework I would like to build. So, with dbolser, another > user in #bioinformatics, we got down to this: > > http://www.bioinformatics.org/wiki/BIOLINUX > > This is indented to be a list of all the bioinformatics tools we know. > Along with a list of "this has a configure script. if not add one". > and a list of "yeah, this is an easy job to package". maybe do a bit > of a butch job and mass-package all the apps that do not have a > package already. > I do not really get it. I find most of those tools already in Debian. bwa, mummer,samtools,velvet are in ... not sure about the state of the others. > as i said, ideas galore :D > > *cough* email about mira tonight *cough* > I do now. We have a working package for it. It is just not yet uploaded to the distribution. svn://svn.debian.org/svn/debian-med/trunk/packages/mira/trunk That packaging is not so very nice, yet, but just give it a chance, please, and, of course, feel free to extend.
Best, Steffen > On Thu, Mar 31, 2011 at 2:56 PM, Steffen Möller <[email protected]> > wrote: > >> Hi George, >> >> this is really the work of Richard+Will at EagleGenomics, i.e. >> two physical meetings with them to bring their scripts and >> insights into a form that would be working with Debian. The >> mail below does not reflect that, sorry. >> >> EagleGenomics runs a very interesting symposium next week [1], >> which not unsurprisingly takes time from the volunteer work >> of theirs. Following that we should have some larger threads to >> brainstorm about community work of ours to close the one or >> other usage gap between what Ensembl provides and the packages >> we already have in our distro. >> >> Please stay in touch with whatever ideas or needs are popping >> up on your side. >> >> Best regards, >> >> Steffen >> >> [1] http://www.eaglegenomics.com/2011/01/symposium2011/ >> >> On 03/30/2011 04:58 PM, George Marselis wrote: >> >>> great job, man. this will def minimize my headaches ... >>> >>> On Wed, Mar 16, 2011 at 1:37 PM, Steffen Möller >>> <[email protected]>wrote: >>> >>> >>>> Dear all, >>>> >>>> we can be very happy to now have Ensembl in our distribution. It is in >>>> experimental since it depends on other packages that are still in >>>> experimental. It is in non-free since we do not yet have Jalview packaged >>>> but Ensembl ships the jalview.jar with it. So, there is some more work for >>>> us to do. >>>> >>>> The bioperl1.2.3 package was once rejected since they did not like my >>>> typical symlink hacks. This might need some extra talking with the >>>> ftpmasters I did not yet find the time for, yet. >>>> >>>> What I'd now aim at are some more tools that use DAS, the distributed >>>> annotation system. But this also depends on the feedback we get on the >>>> Ensembl package, i.e. through the folks at EagleGenomics and other users. >>>> Hm. Actually, we could think about a GSoC project addressing DAS in its >>>> many >>>> flavours. >>>> >>>> So, congratulations to us all >>>> >>>> Steffen >>>> >>>> -------- Original Message -------- Subject: ensembl_57-7_amd64.changes >>>> ACCEPTED into experimental Date: Wed, 16 Mar 2011 09:47:24 +0000 From: >>>> Debian >>>> FTP Masters >>>> <[email protected]><[email protected]> To: >>>> Steffen Moeller <[email protected]> <[email protected]>, Debian Med >>>> Packaging Team >>>> <[email protected]><[email protected]> >>>> >>>> Accepted: >>>> ensembl-bin_57-7_amd64.deb >>>> to non-free/e/ensembl/ensembl-bin_57-7_amd64.deb >>>> ensembl-doc_57-7_all.deb >>>> to non-free/e/ensembl/ensembl-doc_57-7_all.deb >>>> ensembl_57-7.debian.tar.gz >>>> to non-free/e/ensembl/ensembl_57-7.debian.tar.gz >>>> ensembl_57-7.dsc >>>> to non-free/e/ensembl/ensembl_57-7.dsc >>>> ensembl_57-7_all.deb >>>> to non-free/e/ensembl/ensembl_57-7_all.deb >>>> ensembl_57.orig.tar.gz >>>> to non-free/e/ensembl/ensembl_57.orig.tar.gz >>>> libensembl-compara-perl_57-7_all.deb >>>> to non-free/e/ensembl/libensembl-compara-perl_57-7_all.deb >>>> libensembl-core-perl_57-7_all.deb >>>> to non-free/e/ensembl/libensembl-core-perl_57-7_all.deb >>>> libensembl-draw-perl_57-7_all.deb >>>> to non-free/e/ensembl/libensembl-draw-perl_57-7_all.deb >>>> libensembl-external-perl_57-7_all.deb >>>> to non-free/e/ensembl/libensembl-external-perl_57-7_all.deb >>>> libensembl-functgenomics-perl_57-7_all.deb >>>> to non-free/e/ensembl/libensembl-functgenomics-perl_57-7_all.deb >>>> libensembl-variation-perl_57-7_all.deb >>>> to non-free/e/ensembl/libensembl-variation-perl_57-7_all.deb >>>> >>>> >>>> Override entries for your package: >>>> ensembl-bin_57-7_amd64.deb - extra non-free/utils >>>> ensembl-doc_57-7_all.deb - extra non-free/doc >>>> ensembl_57-7.dsc - extra non-free/science >>>> ensembl_57-7_all.deb - extra non-free/science >>>> libensembl-compara-perl_57-7_all.deb - extra non-free/perl >>>> libensembl-core-perl_57-7_all.deb - extra non-free/perl >>>> libensembl-draw-perl_57-7_all.deb - extra non-free/perl >>>> libensembl-external-perl_57-7_all.deb - extra non-free/perl >>>> libensembl-functgenomics-perl_57-7_all.deb - extra non-free/perl >>>> libensembl-variation-perl_57-7_all.deb - extra non-free/perl >>>> >>>> Announcing to [email protected] >>>> Closing bugs: 589818 >>>> >>>> >>>> Thank you for your contribution to Debian. >>>> >>>> >>>> >>> >> >> > > -- To UNSUBSCRIBE, email to [email protected] with a subject of "unsubscribe". Trouble? Contact [email protected] Archive: http://lists.debian.org/[email protected]
