On Fri, Dec 09, 2011 at 01:00:48PM +, Nick James wrote:
> >I'm tempted to kick all files matching "*.h" and "*.cpp" from the binary
> >package where these are pretty useless. This would solve the lintian
> >warnings
> >
> >W: libensembl-core-perl: executable-not-elf-or-script
> >usr/share/ens
On Fri, Dec 09, 2011 at 04:58:46PM +, Nick James wrote:
> Hi Andreas,
>
> Thanks for the instructions. One question, should I be checking out
> the source with write permission:
>
> *svn co* |svn+ssh://u...@svn.debian.org/svn/debian-med/trunk/...
> in which case do I need a username / passw
On Fri, Dec 09, 2011 at 04:56:11PM +0100, Steffen Möller wrote:
> On 12/09/2011 02:02 PM, Andreas Tille wrote:
> > On Fri, Dec 09, 2011 at 11:55:41AM +, Nick James wrote:
> >> I'm happy to look into other things that you are not sure if they
> >> are needed.
> A major reason for Ensembl to rema
Hi Andreas,
Thanks for the instructions. One question, should I be checking out the
source with write permission:
*svn co* |svn+ssh://u...@svn.debian.org/svn/debian-med/trunk/...
in which case do I need a username / password? And commit changes myself.
Or just for reading:
|*svn co* |svn:/
Hi Steffen,
I think both Jalview and Bioperl are issues that need to be raised
upstream.
I think the older bioperl dependency is down to a very small amount of
code. I will raise this with the ensembl team. Obviously that will not
make it until at least the next release ( v66 ). I can ha
Hello,
On 12/09/2011 02:02 PM, Andreas Tille wrote:
> On Fri, Dec 09, 2011 at 11:55:41AM +, Nick James wrote:
>> I'm happy to look into other things that you are not sure if they
>> are needed.
A major reason for Ensembl to remain in the (not so fancy)
"experimental" section is for its depende
On Fri, Dec 09, 2011 at 01:00:48PM +, Nick James wrote:
> >W: libensembl-core-perl: executable-not-elf-or-script
> >usr/share/ensembl/ensembl/misc-scripts/alternative_splicing/AltSplicingToolkit/src/util/StringUtil.h
> >W: libensembl-core-perl: executable-not-elf-or-script
> >usr/share/ensemb
On Fri, Dec 09, 2011 at 11:55:41AM +, Nick James wrote:
> I'm happy to look into other things that you are not sure if they
> are needed. How do I get a list of scripts that are causing
> problems?
The idea is to run lintian on the resulting packages. So how to get
these packages. There are
Hi Andreas,
On 08/12/11 21:56, Andreas Tille wrote:
Hi again,
On Thu, Dec 08, 2011 at 10:02:13PM +0100, Andreas Tille wrote:
Hi Nick,
On Thu, Dec 08, 2011 at 05:24:51PM +, Nick James wrote:
It is what the Ensembl
team use internally for batch submission.
Iven in this case the script loo
On 08/12/11 21:02, Andreas Tille wrote:
Hi Nick,
On Thu, Dec 08, 2011 at 05:24:51PM +, Nick James wrote:
You probably know this, but bsub is the submission command for the
LSF computer cluster submission software.
Well, please do not overestimate my knowledge. I did not worked with
cluste
Hi again,
On Thu, Dec 08, 2011 at 10:02:13PM +0100, Andreas Tille wrote:
> Hi Nick,
>
> On Thu, Dec 08, 2011 at 05:24:51PM +, Nick James wrote:
> > It is what the Ensembl
> > team use internally for batch submission.
>
> Iven in this case the script looks somehow suspicious.
s/I/E/
Nick, i
On Thu, Dec 08, 2011 at 07:43:25PM +0100, Steffen Möller wrote:
> 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 have a local user management". This makes some very
> decent sense for a
Hi Nick,
On Thu, Dec 08, 2011 at 05:24:51PM +, Nick James wrote:
> You probably know this, but bsub is the submission command for the
> LSF computer cluster submission software.
Well, please do not overestimate my knowledge. I did not worked with
clusters so far.
> It is what the Ensembl
>
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
Hi Andreas,
You probably know this, but bsub is the submission command for the LSF
computer cluster submission software. It is what the Ensembl team use
internally for batch submission.
My point is that there are many utility scripts ( like
ensembl-variation/scripts/import/run.me ) hanging a
Hi Nick,
On Thu, Dec 08, 2011 at 03:56:20PM +, Nick James wrote:
> Just a quick post to introduce myself.
> ...
welcome in the team. I think I had your address in CC in my mail
yesterday concerning some Ensembl issues. It would be great if you
could contact Ensembl authors about this. I ho
Hi,
Just a quick post to introduce myself.
I work for Eagle Genomics, an outsourced bioinformatics services and
software company specialising in genome content management and the
provision of open-source solutions.
At Eagle we are intestered in packaging Ensembl, which is widely used
genome
On Thu, 26 Jun 2008, Olivier Langella wrote:
I am new to debian-med and I would like to introduce myself :
Bioinformatics engineer in the "UMR de Génétique Végétale"
(http://moulon.inra.fr/welcomegb.html) and Linux user since the Debian Potato
release, I would be happy to contribute to this gr
Hello,
I am new to debian-med and I would like to introduce myself :
Bioinformatics engineer in the "UMR de Génétique Végétale"
(http://moulon.inra.fr/welcomegb.html) and Linux user since the Debian
Potato release, I would be happy to contribute to this great project
(depending on my skills).
Greetings,
I'd like to introduce myself as a new member of Debian-Med. I'm a Research
Programmer working in Molecular Graphics Laboratory of the The Scripps Research
Institute. I'm a lead developer for Python Molecular Viewer which is distributed
with MGLTools (http://mgltools.scripps.edu). Thank
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