Re: ensembl_57-7_amd64.changes ACCEPTED into experimental
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 <steffen_moeller@gmx.de> 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 <steffen_moeller@gmx.de>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 <ftpmaster@ftp-master.debian.org><ftpmaster@ftp-master.debian.org> To:
>>> Steffen Moeller <moeller@debian.org> <moeller@debian.org>, Debian Med
>>> Packaging Team <debian-med-packaging@lists.alioth.debian.org><debian-med-packaging@lists.alioth.debian.org>
>>>
>>> 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 debian-devel-changes@lists.debian.org
>>> Closing bugs: 589818
>>>
>>>
>>> Thank you for your contribution to Debian.
>>>
>>>
>>
>
>
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