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...
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. as i said, ideas galore :D *cough* email about mira tonight *cough* 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". 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