Re: ensembl_57-7_amd64.changes ACCEPTED into experimental
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 <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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