On Feb 11, 2015, at 9:32 AM, Roland Fehrenbacher r...@q-leap.de wrote:
Anyone can judge the real impact of this?
Other groups have worked on similar capability.
http://bioinformatics.oxfordjournals.org/content/early/2014/02/12/bioinformatics.btu071.abstract
These are essentially
Hello Andreas,
Don’t take my opinion as absolute, but I have used bowtie quite a bit in the
past. According to the manual, for that specific example:
Example 5: -a —best
Specifying -a results in the same alignments being printed as if just -a had
been specified, but they are guaranteed to be
Hello,
On Apr 28, 2014, at 2:32 AM, Andreas Tille andr...@an3as.eu wrote:
[Debian Med list in CC]
Hi Marc,
On Sun, Apr 27, 2014 at 09:57:23AM +0200, Marc Haber wrote:
On Fri, 25 Apr 2014 20:53:01 +0200, Andreas Tille ti...@debian.org
wrote:
Description : efficient mapping of short
Not sure ITP made it to list...
Begin forwarded message:
Resent-From: Scott Christley schrist...@mac.com
From: Scott Christley schrist...@mac.com
Date: March 29, 2012 3:47:18 PM CDT
Resent-To: debian-bugs-d...@lists.debian.org
To: sub...@bugs.debian.org
Resent-Cc: debian-med
Package: wnpp
Severity: wishlist
Owner: Scott Christley schrist...@mac.com
X-Debbugs-CC: debian-med@lists.debian.org
Package name: libkawa
Version : 1.6.1
Upstream Author : Per Bothner p...@bothner.com
URL : http://www.gnu.org/software/kawa/
License : MIT
Hello Andreas,
I enabled the java build within Swarm, it appears to compile correctly and now
I'm working on getting the right files in the package. I've discovered that
Swarm uses KAWA [1] and the kawa.jar file is just included with Swarm. My
understanding is that packages cannot just
Hi Andreas,
Oh sorry, I thought I posted my results but apparently not! The upgrade was a
no go, everything download and installed okay but upon reboot the machine
froze. If I get a chance then I will try to install the testing distribution.
In the meantime, I've been working with upstream
Hi Andreas,
I have committed my changes.
On Mar 7, 2012, at 2:39 PM, Andreas Tille wrote:
So you are working on stable which is fine. Please try
apt-cache policy lintian
It should mention newer versions for testing and unstable. If not
please adapt your sources.list to also mention
will keep on helping to finalise the package
once Luis will confirm success in getting cmake working.
An explicite thanks to Luis who made me realise that MoM might be really
a good idea. There is one new entry in the queue saying
Scott Christley: swarm
(Scott is in CC this time
Hello Chris,
Can you tell me the status of this bug? There are patches available which
correct the segmentation fault, and I need this patched version so the software
I'm packaging [1] will work correctly.
thanks
Scott
[1] http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=611922
--
To
Hello Andreas,
On Jan 19, 2012, at 3:14 AM, Andreas Tille wrote:
Hi Scott,
On Wed, Jan 18, 2012 at 04:07:06PM -0600, Scott Christley wrote:
I have committed a few changes to the swarm package, most notably the
passing of correct parameters to configure, so now the package looks to
build
Hello,
I have committed a few changes to the swarm package, most notably the passing
of correct parameters to configure, so now the package looks to build
completely. However, the deb files are essentially empty. Could somebody
please take a look and give me a hint for how to package shared
===
--- trunk/packages/swarm/trunk/debian/control 2012-01-12 18:52:47 UTC (rev
9268)
+++ trunk/packages/swarm/trunk/debian/control 2012-01-12 21:32:43 UTC (rev
9269)
@@ -6,7 +6,7 @@
Uploaders: Scott Christley schrist...@mac.com,
Andreas Tille ti
On Feb 18, 2011, at 4:13 AM, Andreas Tille wrote:
On Fri, Feb 18, 2011 at 10:22:40AM +0900, Charles Plessy wrote:
there is also the problem that a non-free source package is not allowed to
produce binary packages for the main archive… Perhaps the best solution for
the
moment is to keep the
Hello,
I was looking at the meme packaging and noticed that it hadn't been finished,
so I've made a few changes and have gotten it to build. However I have a
question. MEME is actually a suite of programs. In the current packaging,
there is a separate package for one of the programs
the Jar
files with the softs.
The core e.g. the main program that is called by the web interface will be
in free.
Core can also be used without the web interface, but interface is definitly a
plus
Olivier
Le 2/16/11 5:53 PM, Scott Christley a écrit :
Hello,
I haven't followed
created
by professionals ;) I am talking about complimenting them
whenever feasible/sensible for the Debian needs/purposes.
On Tue, 15 Feb 2011, Scott Christley wrote:
I think putting the data itself into debian repository is problematic.
Regardless of any licensing issue, the shear
wrote:
On Thu, Feb 10, 2011 at 03:44:11PM -0600, Scott Christley wrote:
I just committed the initial packaging for libtecla, ITP bug #612625. I
would be happy if somebody could review my package.
When I run lintian I get these messages, I kinda understand the errors but
am not sure how
Hello,
I have committed the initial packaging for maude into SVN. lintian was clean.
Please review and upload if it looks good!
thanks
Scott
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Archive:
Hello,
I get the following error when trying to build the biomaj debian package from
SVN. Anybody know what the error is? I'm guessing a missing dependency.
thanks
Scott
compile:
[mkdir] Created
dir:
Hello,
I wonder if anybody has thought about providing large data sets, like genomes,
microarray data, etc. into debian packages in a way that makes it easy for
users to get those data sets onto their machine, making it easier to use
various tools? I can think of many great ways this would be
I think putting the data itself into debian repository is problematic.
Regardless of any licensing issue, the shear amount of data is too great.
Better to let the professionals who are getting paid to manage the data (NCBI,
KEGG, etc.) and download directly from those sites. Pretty much all
On Feb 11, 2011, at 8:23 AM, Michael Banck wrote:
On Wed, Feb 09, 2011 at 10:18:15AM -0600, Scott Christley wrote:
Description : Tecla is a command-line editing library
The tecla library provides UNIX and LINUX programs with interactive
command line editing facilities, similar to those
Package: wnpp
Severity: wishlist
Owner: Scott Christley schrist...@mac.com
X-Debbugs-CC: debian-med@lists.debian.org
Package name: libgbfp
Version : 0.6.1
Upstream Author : GreenGene BioTech Inc.
URL : http://code.google.com/p/gbfp/
License : GPL
Programming Lang
Hello,
I just committed the initial packaging for libtecla, ITP bug #612625. I would
be happy if somebody could review my package.
When I run lintian I get these messages, I kinda understand the errors but am
not sure how to resolve. For example, how do I indicate this package closes an
ITP
Package: wnpp
Severity: wishlist
Owner: Scott Christley schrist...@mac.com
X-Debbugs-CC: debian-med@lists.debian.org
Package name: libtecla
Version : 1.6.1
Upstream Author : Martin C. Shepherd m...@astro.caltech.edu
URL : http://www.astro.caltech.edu/~mcs/tecla/
License
I tried adding the X-Debbugs-CC tag in my ITP, but I don't think it worked, the
email I sent is below anybody know what I'm doing wrong?
Scott
Begin forwarded message:
From: Scott Christley schrist...@mac.com
Date: February 3, 2011 3:00:56 PM CST
To: sub...@bugs.debian.org
Subject: ITP
On Oct 2, 2010, at 3:55 AM, Charles Plessy wrote:
Le Thu, Sep 30, 2010 at 08:49:11AM +0200, Andreas Tille a écrit :
when browsing through the list of packages which have incomplete
information in our tasks files I stumbled uppon SequenceConverter.app.
Historically this program once was
BioCocoa is ready for upload! The bits of code under question were re-released
under the Lucent Public License 1.02 which should pass Debian guidelines.
Sorry it took so long!
cheers
Scott
On Apr 23, 2010, at 1:11 AM, Andreas Tille wrote:
On Thu, Apr 22, 2010 at 01:40:43PM -0700, Scott
On Sep 13, 2010, at 4:00 PM, Andreas Tille wrote:
Scott, you once worked on this package. Would you volunteer to prepare
final packages for upload. I'm currently a bit distracted by other
tasks (GNUmed packaging, some Blends infrastraucture things, etc.) For
sure other volunteers are
On Apr 24, 2010, at 9:06 PM, Steve M. Robbins wrote:
On Sat, Apr 24, 2010 at 11:14:31AM -0700, Scott Christley wrote:
Then when I use the svn-b alias (svn-buildpackage -us -uc -rfakeroot
--svn-ignore) the output is this:
chmod a+x
/home/scottc/Projects/tools/debian-med/trunk/packages
On Apr 23, 2010, at 7:43 PM, Scott Christley wrote:
Has anybody put together a package that uses the standard GNU autotools to
configure? Everything I read seems to indicate that the debian/rules file is
very simple, yet it is not working for me. It complains that there is no
configure
Hello,
Has anybody put together a package that uses the standard GNU autotools to
configure? Everything I read seems to indicate that the debian/rules file is
very simple, yet it is not working for me. It complains that there is no
configure file. However, there is definitely a configure
Hi Andreas,
I should have a copy of Jakson's files. I was using them to give me hints for
packaging Swarm. The upstream Swarm code has changed significantly so the
packaging needs to be updated. I have the files in my local Debian Med
checkout, so I suppose I should commit them sometime
On Apr 22, 2010, at 2:29 PM, Andreas Tille wrote:
On Thu, Apr 22, 2010 at 01:50:10PM -0700, Scott Christley wrote:
Hi Andreas,
I should have a copy of Jakson's files. I was using them to give me hints
for packaging Swarm. The upstream Swarm code has changed significantly so
On Oct 7, 2009, at 10:24 PM, Andreas Tille wrote:
would you mind contacting upstream about this issue because you are
obviousely well informed ?
Yes, will do.
Scott
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On Sep 21, 2009, at 12:31 AM, Andreas Tille wrote:
On Sun, Sep 20, 2009 at 07:18:02PM -0700, Scott Christley wrote:
A new upstream release of BioCocoa. The package should be completely
covered by a BSD style license, so hopefully all of the license
issues
are resolved now. I've updated
might just want to rewrite those functions.
thanks
Scott
On Oct 7, 2009, at 1:08 PM, Andreas Tille wrote:
On Wed, Oct 07, 2009 at 10:55:20AM -0700, Scott Christley wrote:
Is there any way to check status of upload?
The maintainer gets information about the status. In our case
Both are agent-based simulation toolkits. I'm not sure which category
that fits under but in general they are discrete-time (or discrete-
event) simulators, typically stochastic. Agent-based is more a
modeling methodology versus a simulation technology.
The recent issue of Nature has a
I'm definitely interested in Swarm; I'm very familiar with it. It
does have Java but it is mainly Objective-C, the Java part is extra.
I am also familiar with Repast though not as much.
If somebody would like to work with me to package them, I will
definitely help.
cheers
Scott
On Aug
I wonder what the current status of Biococoa.app might be.
Scott Christley has split up a separate application
sequenceconverter.app
but neither a new biococoa.app nor sequenceconverter.app was finally
uploaded.
Scott could you please elaborate on your plans for an upload? Any
blockers
we
Hey Charles,
I've done GSoC for the Swarm Development Group the last two years.
The first year we got three students, I mentored two of them. Last
year I volunteered to mentor, but we got only two students and my
projects didn't get picked.
We took both approaches, we listed a lot of
On Oct 18, 2008, at 7:00 AM, Charles Plessy wrote:
just let us know when updated packages are available. Also, if you
want
to make stronger tests of your biococoa package, you can try to
package
your software for ultraconserved elements, depending on your updated
biococoa package, and test
Hello,
There is a software package called Swarm (http://www.swarm.org) which
is an agent-based simulation toolkit that I would like to package into
Debian. Is debian-med interested in modeling and simulation
software? Systems biology? Or do you think there is another more
appropriate
Hello Charles,
On Oct 15, 2008, at 5:04 PM, Charles Plessy wrote:
nice work ! Now we have working BioCocoa and SequenceConverter
packages :)
Would you like to add your name in the 'Uploaders:' field of
debian/control and become maintainer of them?
Ok, sure.
I have two other unrelated
On Oct 12, 2008, at 10:54 PM, Charles Plessy wrote:
Le Sun, Oct 12, 2008 at 03:57:33PM -0700, Scott Christley a écrit :
So I got BioCocoa to produce a new source code release, and worked on
modifying the package files. The patch is not very big so I've
attached
it. This is my first
On Oct 13, 2008, at 1:21 AM, Charles Plessy wrote:
Le Sun, Oct 12, 2008 at 11:40:11PM -0700, Scott Christley a écrit :
The sequence converter code doesn't seem to compile with version 2.X,
so I think it needs to either be rewritten or maybe functionality is
missing from 2.X, I'm not sure
Hello,
So I got BioCocoa to produce a new source code release, and worked on
modifying the package files. The patch is not very big so I've
attached it. This is my first attempt, so I welcome any comments.
The resultant deb installs fine, and I compiled some code against the
installed
, I will retry.
cheers
Scott
On Sep 27, 2008, at 6:55 PM, Scott Christley wrote:
Okay, ran into my first issue. I checked out the Debian Med svn
repository, got the latest BioCocoa source code put into a tarball,
and am now trying the svn-buildpackage command. It gives me an error:
dpkg
Greetings,
Thanks to Charles Plessy for directing me to this list.
I am a developer for BioCocoa, which is an GNUstep framework for
bioinformatics, and I would like to have BioCocoa provided as a Debian
package. My understanding is there is an existing package,
biococoa.app, but it is
Okay, ran into my first issue. I checked out the Debian Med svn
repository, got the latest BioCocoa source code put into a tarball,
and am now trying the svn-buildpackage command. It gives me an error:
dpkg-checkbuilddeps: Unmet build dependencies: libgnustep-gui-dev (=
0.12.0)
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