Agreed. And then there is this ever-lasting issue about the uncertainty
what our home page should be.
Personally, I do not mind to leave much of the direct user interaction
with BioLinux, much like Ubuntu taking a lot from us. I am more
concerned about the synchronicity of our packaging.
So, once
On 03/15/2012 02:36 PM, Yaroslav Halchenko wrote:
Agreed. And then there is this ever-lasting issue about the uncertainty
what our home page should be.
yeah -- I always just google debian-med and choose one which fits me
best
:) I just use (some of) the packages ...
IMHO ideally it should
On 03/15/2012 03:09 PM, Yaroslav Halchenko wrote:
IMHO ideally it should be something easy to remember e.g.
med.debian.net ? ;)
And bio.debian.net as an alias :) Just kidding. Somewhat. I would
support your suggestion.
;-)
My hunch is that we need an exchange about the practical side
Hello,
On 03/13/2012 07:42 PM, Thorsten Alteholz wrote:
according to http://valdarlab.unc.edu/software.html bagphenotype is no
longer maintained and shall be replaced by bagpipe. What shall we do?
bagphenotype is not in the distribution and I think it should not for
the time being. It is too
On 03/08/2012 10:00 AM, Andreas Tille wrote:
On Thu, Mar 08, 2012 at 09:48:03AM +0100, Johan Moreau wrote:
Le 07/03/12 11:57, Andreas Tille a écrit :
Andreas thank you for this message. The workshop about packaging medical
applications for Debian is a good idea. I will try to find a room.
Hello,
On 03/05/2012 08:18 AM, Andreas Tille wrote:
is this something we should suggest for biologists?
Somewhat on the periphery. I suggest to leave it with Debian Science.
Best,
Steffen
(new) lammps-doc_0~20120228.git268a14f-1_all.deb extra doc
Molecular Dynamics Simulator. Documentation
Hello,
On 02/27/2012 05:58 PM, Alan R Williams wrote:
We (the myGrid team at Manchester) have had an e-mail from the Open
Invention Network - http://www.openinventionnetwork.com .
I'm seeking other people's opinion about if the patent portfolio
initiative is a good thing and whether it is
Today, Amazon started its simple workflow system - an integration of
one's cloud-or-home-run applications:
http://www.allthingsdistributed.com/2012/02/Amazon-Simple-Workflow-Service.html
I do not know what this means to us, yet. Let opinions fly in.
Cheers,
Steffen
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Hello,
I just received this invite to submit papers. I did not read them to be
Open, but they are free (as in beer, if beer was any healthy) at least.
Well, they are a bit blank, still.
Anyway, only following it with half an eye, I am excited about the progress
the medical side of Debian Med is
Hello,
The annual Bioinformatics Open Source Conference (BOSC) since Boston
comes with premeetings, the Hackathons or Codefest. This year, BOSC [1]
is in California, and thus out of reach for many volunteer contributors
to Open Source Biology. So, some brave folks came up with the idea to
have a
On 02/21/2012 03:50 PM, Andreas Tille wrote:
I admit I can not give any sure confirmation whether I will join or not
but there is a 60% chance that I will show up at this event. I'm
specifically interested in extending the time over the weekend
(21.+22.7.) as it is suggested unofficially.
Dear Scott,
Thank you for your stimulating request. I feel reminded about some grid
computing past of mine and dynamic runtime environments.
From what I observe, though, those technologies never were adopted (beyond
experimental stages) for heterogeneous setups like
those in bioinformatics. I
Hello,
this is a friendly community addressing issues in next generation sequencing
http://seqanswers.com
and there is a NAR paper on it
http://nar.oxfordjournals.org/content/early/2011/11/15/nar.gkr1058.abstract
I liked how they communicate in their forum. And it also rendered it very
Hi Mark,
It is great to see Fiji approaching
On 01/07/2012 02:31 PM, Mark Longair wrote:
I was very happy about your proposal to start a rearrangement of
Fiji that is DFSG compliant. In parallel to that, I would like to discuss
the possibility to upload more or less what you have with
Hello,
On 01/03/2012 10:16 PM, Eric Maeker wrote:
Is it possible to add new package in the actual debian stable 0.6.3 ?
Or should new package be build using testing ?
That make a big difference for us because Qt4 versions are not the
same (and code must be adapted).
It should be possible to
On 12/19/2011 09:43 AM, Andreas Tille wrote:
On Mon, Dec 19, 2011 at 12:40:58AM +0100, Steffen Möller wrote:
I actually very much in favour of building mgltools from plain upstream
source as it is provided upstream in one source package and create
different source packages. When doing
On 12/18/2011 12:23 AM, Andreas Tille wrote:
On Sat, Dec 17, 2011 at 10:13:05PM +0100, Steffen Möller wrote:
I just tried to install mgltools-pmv in sid and autodocktools was installed
as well. So there should be no problem for the user
but the cycle still seems to be present
On 12/16/2011 07:22 PM, Thorsten Alteholz wrote:
Hi Andreas,
On Wed, 7 Dec 2011, Andreas Tille wrote:
Resolved circular dependency by recommending autodocktools instead from
depending from it. In case there *really* should be a strong dependency
this is not the correct fix and we need
On 12/15/2011 01:24 PM, Andreas Tille wrote:
On Thu, Dec 15, 2011 at 11:47:23AM +0100, Steffen Möller wrote:
The license is the typical non-commercial one. I spoke with
Nick Patterson from upstream, a Debian user himself, who is happy
with us redistributing their work.
Did he said that he
On 12/15/2011 04:30 PM, Andreas Tille wrote:
On Thu, Dec 15, 2011 at 02:47:53PM +0100, Steffen Möller wrote:
On 12/15/2011 01:24 PM, Andreas Tille wrote:
The license is the typical non-commercial one. I spoke with
Nick Patterson from upstream, a Debian user himself, who is happy
with us
On 12/15/2011 04:32 PM, Andreas Tille wrote:
On Thu, Dec 15, 2011 at 03:59:15PM +0100, Eric MAEKER wrote:
I suggest someone to take the management of this list. The
manager will be the one who contact each upstream of our
medicalsrelated project to subscribe and discuss. If no one
wants this
Ivo, Mathieu,
On 12/09/2011 10:50 AM, Mathieu Malaterre wrote:
On Fri, Dec 9, 2011 at 10:45 AM, Ivo Maintz i...@maintz.de wrote:
after spending some time by packaging cellprofiler myself, I discovered
your (not finished) package. What do you think about merging our
approaches? I mainly got it
Hello,
On 12/08/2011 06:24 PM, Nick James wrote:
My suggestion is that we just ignore this script as it is not needed
for Ensembl to run.
We should decide over time what it means for us to see Ensembl run.
The current definition for our package seems to be use the public data
of Ensembl but
:) This is quite some cross-posting.
On 11/25/2011 08:39 PM, Eric Maeker wrote:
Le 25 novembre 2011 17:32, Karsten Hilbert karsten.hilb...@gmx.net a écrit :
On Fri, Nov 25, 2011 at 05:05:31PM +0100, Eric Maeker wrote:
While I agree the logical and lofty goal would be to create
a Linux
Dear all,
our lab's sample management does not scale and needs an overhaul. The
idea is to migrate to an Open Source solution that fits the core needs
(what sample sent by whom in what form in what freezer last used by whom
for what project) and then have this adapted to our further needs.
needs
Hi Christoph,
I also looked here
https://support.quest.com/Search/ProductInformation.aspx?dsNav=Ns:P_DateLastModifiedSortable|101|-1|,Nea:True,N:268438638-4294962718Dt=JClass
and it does not look good. I suggest to spare the energy of packaging
openastexviewer for the time being. For
On 11/10/2011 09:21 AM, Andreas Tille wrote:
On Thu, Nov 10, 2011 at 08:49:11AM +0100, Sebastian Hilbert wrote:
I am currently working with upstream to get some problems corrected. Turns
out
that part of the problem is that e.g. ITK would need patches.
How would you consider the chances
Hello,
On 11/03/2011 09:06 PM, Mathieu Malaterre wrote:
Hi Mark,
On Thu, Nov 3, 2011 at 5:14 PM, Mark Longair
mark-debianli...@longair.net wrote:
[...]
Unfortunately, I believe that my current approach to creating
the Fiji Debian packages is the wrong one, and it might be worth
taking a
Hi Tony,
On 10/27/2011 01:14 PM, Tony Travis wrote:
On 26/10/11 18:12, Steffen Möller wrote:
Heyho,
During the 1980's, I commissioned a 9216 processor CLIP4R (Cellular
Logic Image Processor) SIMD array built for the MRC by the Rutherford
Appleton labs. This used FPGA's and custom LSI
Dear all,
Strolling through the ISMB exhibitors hall in Vienna I got in
contact with the company SciEngines [1]. They are a
not-so-recent-anymore startup from a neighbouring University,
i.e. a bunch of electroengineers crafting themselves from
A to E and G to Z the FPGA-cards for application
On 10/11/2011 01:43 PM, Andreas Tille wrote:
On Tue, Oct 11, 2011 at 06:43:15PM +0900, Charles Plessy wrote:
I am trying to build such an image from the bottom up, and unfortunately I am
blocked at the partitionning during the execution of the Debian Installer.
Hello,
what came to mind was:
* What are your peers using? The suggestion to use a virtual setup
makes perfect sense. I would try multiple distros and decide which you
like best ... and tell us :)
* How good is your internet access? Are clouds to which to log in
remotely an option?
Concerning
On 09/26/2011 12:07 PM, Charles Plessy wrote:
Le Mon, Sep 26, 2011 at 11:31:15AM +0200, Luca Capello a écrit :
Given that ncbi-blast+ provides a 'legacy_blast' script without the .pl
extension, the ncbi-blast+-legacy package should reflect that.
Dear all,
I would like to take the opportunity
On 09/16/2011 02:48 PM, Laszlo Kajan wrote:
I have two new packages: libzerg and libzerg-perl: fast Blast parser library
and module:
It's fine. I'll go through it all over the weekend.
Have many thanks for your efforts, best regards,
Steffen
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On 09/14/2011 09:25 PM, Andreas Tille wrote:
On Wed, Sep 14, 2011 at 07:48:21PM +0200, Thorsten Alteholz wrote:
I just found out that package abyss is currently not maintained within
Debian Med but still in the svn repository. As there are currently
several methods to mark packages no
Dear Charles,
On 09/05/2011 02:33 AM, Charles Plessy wrote:
Le Sun, Sep 04, 2011 at 08:55:52PM +0200, Steffen Möller a écrit :
What are we doing when one package has multiple publications assigned,
say each announcing a particular development? Ensembl could be such,
where there is one
Hi Olivier,
On 09/05/2011 07:59 AM, Olivier Sallou wrote:
[...]
My basic question to you guys now would be
0) do you share the vision that the packages should come with
instructions how to get the data, not the getData package itself?
This is a difficult point. Data location/format may
Hello,
Jakub had found the dependency on numpy to be missing. This was weird
since this should have been found as a binary dependency through the
shlibdeps. The bell then only rang when the newly introduced -dbg
package remained empty: the libs where not installed but remained
quietly in
This is a bit more for debichem or debian-science, but mentioned
in the autodock tips'n'tricks documentation. Well, just any volunteer
for packaging
http://kinemage.biochem.duke.edu/software/reduce.php
would be most welcome.
The package is free in some GNU sense but has a custome 5-10
Hello,
this very early morning I had prepared getData [1] configs to download the
descriptions of ligands for docking with autodock. It
was motivated as a followup to that Google Summer of Code project to prepare
explicit instructions for setting up a BOINC server
with Debian for molecular
On 09/04/2011 04:19 PM, Michael Banck wrote:
Hi,
On Sun, Sep 04, 2011 at 12:23:04PM +0200, Steffen Möller wrote:
This is a bit more for debichem or debian-science, but mentioned
in the autodock tips'n'tricks documentation. Well, just any volunteer
for packaging
http
Hello,
What are we doing when one package has multiple publications assigned,
say each announcing a particular development? Ensembl could be such,
where there is one publication announcing Compara, and something else
maybe ... your feature of choice.
I am now running into an issue with my
Hello,
is anybody using
http://www.tm4.org/
and would be interested to start packaging (pieces of) it?
Many greetings
Steffen
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Archive:
On 08/29/2011 09:05 AM, Andreas Tille wrote:
Hi Olivier,
On Mon, Aug 29, 2011 at 08:39:41AM +0200, Olivier Sallou wrote:
Hi, There are some gbrowse build (test) failures on a few archs, on
05-defferedrendering.t . This group of test seem to randomly fail on a
few tests (armel last time, an
On 08/26/2011 12:41 PM, Tim Booth wrote:
Hi Steffen,
we have qiime in experimental because of pynast from what I recall.
I have not moved that into non-free/sid.
I'd forgotten about PyNAST. I can't see any licensing reason why it
can't go into Sid. I've had a play with it just now and
Hello,
Andreas and I have different opinions on the forwarding of posts to
http://debianmed.blogspot.com to http://planet.debian.org/ . I would
like to have those entries that shall be forwarded to be tagged with
the label 'planet'. The labels can be added any time if they have
been forgotten
Dear all,
with BioMAJ [1] and getData [2], our distro has now two tools in the
distribution that address the retrieval and post-processing
of public (or not so public) databases. Hilmar from the OBF has just pointed me
to an again very different approach towards the
same by the Open Knowledge
Hello,
On 08/22/2011 05:15 PM, Michael Banck wrote:
the latest debian-med blog post (syndicated on Planet Debian, CC'd)
http://debianmed.blogspot.com/2011/08/experimenting-with-amazon-cloud-and.html
has raised some eyebrows.
First off, it should be somehow stated which person wrote/posted
On 08/18/2011 04:53 PM, Aaron M. Ucko wrote:
Olivier Sallou olivier.sal...@irisa.fr writes:
I will try to have a look to patch this in the package. However I will
go on vacation end of this week. So it will not be done before some time...
No problem, the current packaging ignores test
Hello,
@Tim, do not fix the date too stricktly too early, find the right
venue first. From the feedback I got it was important to have
an opportunity for those nightly hacking session, i.e. to have
the bed right next to our venue. Not every place will allow for
that and when there is some sudden
On 08/11/2011 01:39 PM, Andreas Tille wrote:
On Thu, Aug 11, 2011 at 01:33:37PM +0200, Steffen Möller wrote:
venue first. From the feedback I got it was important to have
an opportunity for those nightly hacking session, i.e. to have
the bed right next to our venue.
+ high bandwidth stable
Hello, great to hear from you on all this. Sorry for this bad experience with
the release mixing. You did not ruin your machine
now, I hope.
Two and a half things come to mind (besides the updating of the server):
a) we get those backports done
b) you get a chroot environment for gbrowse of a
Dear Tim,
Have many thanks for raising this issue. It is weird. But this
is exactly why we have this list IMHO.
On 08/03/2011 10:48 AM, Tim Booth wrote:
Hi,
Creating a static package would be easy, but would double the size
(which is large) for blast+ on servers,
Actually, it makes it
Hi Andreas,
On 07/31/2011 06:57 AM, Andreas Tille wrote:
before I'll blog a report about the Debian Med BOF @ DebConf (probably
not before Tuesday when I'm back home) I would like to call for your
help. I had lunch with a journalist which was hopefully interesting
enough for him. He
Hello,
I have auto-created a man page for AutoLigand (debian/autoligand.1), a tool somewhat hidden in the AutoDockTools package and then
edited that. Well, it is not so nice, yet. I'd want to leave that for the next Google code-in (school kids being introduced to
Open Source). When there are
Hello,
I can give it a try.
On 07/29/2011 10:39 AM, Peter Rice wrote:
It might make things clearer if someone from Debian could explain:
(a) why a Creative Commons licence is an issue for you
the OK to fiddle with source code and give it away again is the core
principle of free software.
On 07/04/2011 05:34 PM, Karsten Hilbert wrote:
On Sun, Jul 03, 2011 at 09:42:23PM +0200, Steffen M�ller wrote:
Protege is of interest, too. We have a package for its reasoner Fact++,
due to be updated, admittedly.
If the above means you've been thinking about packaging
Protege, one of the
On 07/03/2011 09:27 AM, Mathieu Malaterre wrote:
Does anyone knows about projects related to ontologies ? Here is the
original email (*).
There is a series of tools helping with data for GeneOntology-like databases.
I had a look at packaging OBOEdit, but this (as usual for Java based tools)
Hello,
the requests for updates of wxWidgets are rather long standing with
pointers to reverse dependencies by rather prominent tools. Upstream
seems to be very Debian/Ubuntu-friendly
http://wiki.wxpython.org/InstallingOnUbuntuOrDebian
and Ubuntu has the packages already.
Is there anybody on the
Hello,
I just read an announcement of the GMOD workshop in San Diego (January,
2012) http://www.intl-pag.org/19/19-gmod.html featuring a session on
MAKER http://gmod.org/wiki/MAKER , their genome annotation environment.
This environment might be an excellent opportunity to interlink our
current
On 06/08/2011 05:14 PM, Olivier Sallou wrote:
Hi Charles,
I see your are the maintainer of bioperl, do you plan to go to version
1.6.901 ?
This version is available on CPAN, and is required to further updates of
gbrowse
Have I missed emails on this? I don't foresee the consequences of an
Hi Thorsten,
On 06/07/2011 10:43 PM, Thorsten Alteholz wrote:
Hi Olivier,
On Tue, 7 Jun 2011, Olivier Sallou wrote:
Can someone have a look and upload to ftp master ?
Over the weekend I'll sponsor everything that is left.
I have to admit that I am not a blast expert so please excuse if I
Hello,
On 06/04/2011 06:48 PM, Thorsten Alteholz wrote:
thanks for all your tips.
I think I am almost finished now with the copyright file. The only open issue
is with file src/cadxcore/xmlrpc/base64.h
The author of this file is listed but there is no license mentioned. Strictly
speaking one
Hello,
On 05/31/2011 11:08 PM, Andreas Tille wrote:
[...]
What will be the next steps? Shall I build the package and upload it
somewhere? What about the svn tag? Shall it be done now or after the
upload?
There is no
immediate
need for an upload - we just have access to SVN and can
On 05/30/2011 10:49 AM, Olivier Sallou wrote:
Hi,
I have 2 questions on ubuntu backport on debian-med launchpad:
1) can we put a package, simply to get it available on current ubuntu
version? (though deb package will be available on next ubuntu release).
If yes, how do we manage it from
Hello,
On 05/27/2011 10:06 AM, Andreas Tille wrote:
I've got a hint from Christoph Gille to include STRAP[1] into Debian.
Indeed. I had a couple of students who came up with STRAP
by themselves to get alignments with structures together,
much like Cn3D ... or Jalview.
He consideres STRAP as
On 05/27/2011 07:54 PM, Thorsten Alteholz wrote:
On Thu, 26 May 2011, Andreas Tille wrote:
What exactly is the problem / error message if you try to commit?
It is still something like:
(...)
Sending trunk/debian/rules
Transmitting file data .svn: Commit failed (details follow):
svn:
Hello,
thank you all for your work on this.
On 05/26/2011 10:18 AM, Andreas Tille wrote:
W: ginkgocadx: postinst-has-useless-call-to-ldconfig
W: ginkgocadx: postrm-has-useless-call-to-ldconfig
That's a usual warning in connection with the rpath issue.
E: ginkgocadx:
Hello,
On 05/23/2011 06:01 AM, Heddle Weaver wrote:
Free medical icons, anybody?
http://www.goomedic.com/free-60-medical-icons-for-medical-apps-developers-and-designers.html?utm_source=feedburnerutm_medium=feedutm_campaign=Feed%3A+Goomedic+%28GooMedic.com%29
Done up by my friend, Hamzamu, an
Hello,
On 05/22/2011 07:13 AM, Sebastian Hilbert wrote:
Am Sonntag, 22. Mai 2011, 01:19:50 schrieb Karsten Hilbert:
On Wed, May 11, 2011 at 08:21:20PM +0200, Steffen M�ller wrote:
[]
What most likely could be done today is to create an experimental
non-free project. Then you can just go
On 05/11/2011 08:43 PM, Karsten Hilbert wrote:
On Wed, May 11, 2011 at 08:21:20PM +0200, Steffen M�ller wrote:
Sebastian, when there are issues, please raise them.
We need Ginkgo CADx :-)))
I had a look and agree, we need that. Just allow the comment that
Ubuntu does not yet have it
Hello,
On 05/19/2011 08:16 PM, Thorsten Alteholz wrote:
I did some work on smile (which I had to rename to biosmile, as there are other
(not yet official) packages already named smile).
From my point of view it is lintian clean and buildable by pbuilder. Can
one of you please have a look
On 05/14/2011 05:16 PM, Tony Travis wrote:
On 14/05/11 14:33, Charles Plessy wrote:
Dear all,
I am preparing to upload r-bioc-biobase soon. It mentions the BioC cran2deb
effort in its description and README:
+++ b/debian/README.Debian
+Unofficial auto-built Bioconductor packages for Debian
On 05/12/2011 11:01 AM, Sebastian Hilbert wrote:
Am Donnerstag, 12. Mai 2011, 10:31:21 schrieb Olivier Sallou:
it is on public one, with oneiric release (next one).
https://launchpad.net/ubuntu/+source/gbrowse/2.26~dfsg-3
It may be just a matter a sync between dependencies, but I do not know
On 05/11/2011 08:11 PM, Sebastian Hilbert wrote:
Am Mittwoch, 11. Mai 2011, 16:59:46 schrieb Dominique Claver KOUAME:
Dear all,
We want to select a software for managing our clinic. We prefer
opensource softwares, and we have discovered debian-med. We want to
know how we can install it on
On 05/11/2011 09:34 PM, Andreas Tille wrote:
On Wed, May 11, 2011 at 08:21:20PM +0200, Steffen Möller wrote:
Why? I always understood Debian Med to support both kinds of UNIXes, Debian
_and_ Ubuntu.
Am I too old? Or has anybody actually grasped the Country and Western Blues
Brothers pun
Hi Olivier,
On 05/09/2011 09:31 AM, Olivier Sallou wrote:
Hi,
I need a sponsor to push biomaj-watcher to FTP master.
biomaj-watcher is the graphical front-end of Biomaj.
Andreas did the job for Biomaj but will lack of time for this one.
I can go for it.
Steffen
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On 05/01/2011 08:42 PM, Tony Travis wrote:
On 29/04/11 22:20, Steffen Möller wrote:
[..]
Hi, Steffen and Will.
I originally wrote this to help me port Bio-Linux4 to Ubuntu 6.06 LTS, but I've
used it with all versions up to and including
Bio-Linux6 and Ubuntu 10.04 LTS. I'm using it right now
Have you set
svn propset mergeWithUpstream 1 debian
?
Cheers,
Steffen
On 04/29/2011 11:28 AM, Olivier Sallou wrote:
Hi,
I have an issue in my packaging build . If someone could help or give
some hints.
In my ncbi-blast-plus packaging, I can do a fakeroot debian/rules
clean/binary.
Hello,
On 04/27/2011 02:35 PM, Olivier Sallou wrote:
I see in tasks the ncbi Blast+ software, not packaged.
Has anyone started something? Or should I go for it
packages/ncbi-tools-cxx
I once had a closer look at ... but then there was something
with the build the let me stop ... don't
Hi Tim,
On 04/27/2011 04:54 PM, Tim Booth wrote:
I'm cracking on with a package for AmpliconNoise, which I can't see any
activity for though there is a placeholder on tasks/bio.
Great!
My
understanding is that a Debian Developer should OK the package
only for a first upload to the release
On 04/26/2011 04:08 PM, Olivier Sallou wrote:
Hi,
I have made my first patch for Biomaj, after it is uploaded in Debian repo.
Could someone please confirm, to help me doing the things correctly.
I have in Debian bugs 2 bug ids (1 bug, 1 wishlist).
I fixed the first with a new patch (quilt)
On 04/19/2011 01:26 PM, Andreas Tille wrote:
On Tue, Apr 19, 2011 at 01:45:48PM +0300, George Marselis wrote:
Hey guys,
I am working on GMOD ( http://gmod.org/wiki/Main_Page ). As you can
see for yourselves, that page was not created with a technical guy in
mind. I need to make a summary of
/2011 05:10 PM, William Spooner wrote:
Could you register debianmed.blogspot.com? I would be happy to guest-post on
Ensembl.
Will
On 18 Apr 2011, at 14:32, Steffen Möller wrote:
On 04/18/2011 02:51 PM, William Spooner wrote:
So Vanessa is coordinating @DebianMed twitter? I'll try
On 04/18/2011 02:51 PM, William Spooner wrote:
So Vanessa is coordinating @DebianMed twitter? I'll try to remember to
include @DebianMed if I post any relevant tweets. I think twitter works best
for conversational items rather than announcements (RSS feeds are much better
for the latter).
Vincent,
I am just CCing Debian Med with this fantastic news. Have man thanks
for your efforts.
Happy
Steffen
Original Message
Subject:Bug#507436: Update...
Resent-Date:Tue, 12 Apr 2011 20:45:02 +
Resent-From:Vincent Fourmond fourm...@debian.org
Resent-To:
Hello,
On 04/12/2011 04:20 PM, Charles Plessy wrote:
Le Tue, Apr 12, 2011 at 02:22:50PM +0200, Olivier Sallou a écrit :
I have updated gbrowse to move db related data to /var/lib instead
of /usr/share
I removed call to metadb_config script and updated config to disable
user management by
/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_moel...@gmx.de
wrote:
Hi George,
this is really the work of Richard+Will at EagleGenomics, i.e.
two
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
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
Dear all,
a week ago or so I had worked on a first (so I had thought) package for the
assembler MIRA. I invested a couple of hours into it and eventually got
it to compile. Only today I then learned that MIRA is also on git:
http://git.debian.org/?p=debian-med/mira.git;a=summary
. The effort is
On 03/09/2011 04:28 PM, Andreas Tille wrote:
On Wed, Mar 09, 2011 at 11:46:35PM +0900, Charles Plessy wrote:
for the prospective packages, I think that the best is to document them as
early as possible in the tasks files,
Yes!
Currently mira is mentioned on the tasks pages tp be in
Hello,
I was proposing as a Google Summer of Code project to experiment about
extending our blends infrastructure towards those packages
that are not DFSG free and that are not even redistributable, but that may be
compiled locally with a happy upstream when there
are patches coming in. Such
Hello,
On 03/03/2011 02:14 PM, Andreas Tille wrote:
when inspecting the URL which was mentioned as Dotur homepage on our Blends
pages it said:
http://schloss.micro.umass.edu/software/dotur.html
Please use mothur instead, feel free to contact Pat Schloss for more
information.
...
in some earlier version ...
Best,
Steffen
Original Message
Subject: [med-svn] r6158 - trunk/packages/wgs-assembler/trunk/debian
Date: Thu, 3 Mar 2011 14:42:31 +
From: Steffen Möller moel...@alioth.debian.org
To: debian-med-com...@lists.alioth.debian.org
Author: moeller
Date
Hello,
On 03/01/2011 12:26 AM, Tony Travis wrote:
On 28/02/11 22:19, Andreas Tille wrote:
[...]
Does it make sense to recalculate a Bioconductor deb repository over
and over instead of just mirroring the result of one single cran2deb
run which would be (re)done in a reasonable frequence?
On 02/26/2011 12:09 AM, Tony Travis wrote:
On 25/02/11 19:55, Manuel Prinz wrote:
On Tue, Feb 22, 2011 at 10:34:41PM +, Tony Travis wrote:
If you want me to name some important Bioconductor packages I use
then I suggest simpleaffy and its dependencies:
On 02/26/2011 10:12 PM, Andreas Tille wrote:
On Sat, Feb 26, 2011 at 01:59:51PM +0100, Karsten Hilbert wrote:
Does this not mean that there ought to be a more convenient way for
users to discover that they need to activate an additional repository
(say, by somehow providing pointers from dummy
I like what I saw about biomaj. What is cannot do for the
moment (from what I understood) is to express a runtime
dependency against a particular database version and have
that then installed package trigger biomaj to perform
that step. Correct me if I am wrong, please. Could that be
added?
What
Hello,
On 02/16/2011 06:00 PM, Scott Christley wrote:
The web interface will have togo to non-free 'cause it depends on several GWT
libraries which are not packaged for Debian so we need to provide the Jar
files with the softs.
I once sponsored backported core gwt packages from Ubuntu to
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