Dear sir,
I'm writing on behalf of the Debian Med project which tries to assemble Free
Software for bio-medical research in a ready to install form inside the
Debian GNU/Linux system (and thus as a consequence into Ubuntu). Your
product TraceViewer is one of the best sequence chromatography tool
Hi.
On 13/02/2011 21:33, Andreas Tille wrote:
then add the following to the classpath
${deblib}/freehep-graphicsio-pdf.jar
${deblib}/freehep-graphicsio-ps.jar
I did so and this has solved 4 out of 10 errors. The remaining ones are
concerning EMF, SVG and SWF (see build log at the URL
Hi,
I have updated biomaj to include commons-cli2 source with biomaj and to
build the jar at packaging time.
In the future, we plan to remove this dependency to avoid issues with
this lib.
I still have some work on biomaj-watcher for same reasons (included
jars), but you can check biomaj
Hi Olivier
On Tue, Feb 15, 2011 at 12:18:18PM +0100, Olivier Sallou wrote:
Hi,
I have updated biomaj to include commons-cli2 source with biomaj and to
build the jar at packaging time.
I have seen your changes in SVN and will have a look soon(ish).
In the future, we plan to remove this
Hi Charles,
On Tue, Feb 15, 2011 at 03:33:03PM +0900, Charles Plessy wrote:
I will package some bioinformatics tools called FASTX-Toolkit, and they
require a separate library, gtextutils, which is used only by them. But
since it is distributed as a separate tarball, the simplest is still
to
Hi Gio,
On Tue, Feb 15, 2011 at 12:15:26PM +0100, Giovanni Mascellani wrote:
Unfortunately, when the answer is trivial you can spend hours on the
code without finding anything.
Yes, as always! Thanks for opening my eyes.
Executing 'ant -verbose' would have
helped: you were just mistyping
Hi,
regarding biomaj-watcher, I cannot remove jar dependencies, as many are
not packaged for Debian (though under open source license). I did a try,
but it is too difficult to get all those libs from source
and compile them with the biomaj-watcher (lots of libraries
dependencies, env setup
Le Tue, Feb 15, 2011 at 01:28:18PM +0100, Andreas Tille a écrit :
Hi Charles,
On Tue, Feb 15, 2011 at 03:33:03PM +0900, Charles Plessy wrote:
I will package some bioinformatics tools called FASTX-Toolkit, and they
require a separate library, gtextutils, which is used only by them. But
Hi Olivier,
On Tue, Feb 15, 2011 at 02:14:26PM +0100, Olivier Sallou wrote:
Hi,
regarding biomaj-watcher, I cannot remove jar dependencies, as many are
not packaged for Debian (though under open source license). I did a try,
but it is too difficult to get all those libs from source
and
I think Mr Lo did not see that the debian-med emailing list is
included in the cc: :)
I was praising Mr Lo, in hopes that I would flatter him enough to
release the SOAPdenovo code under the GPL :D
What he means by using your's resource to compile the latest
version, is that he hopes that KAUST
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
Hi Scott,
I think your idea is quite reasonable in principle. As far as I
understood (but I did not dived into this) the getData effort[1] is one
step into this direction and the to be soon uploaded package Biomaj does
something that might be helpful as well.
Regarding to actually buold
just few cents. In the domain of neuroimaging we are also confronted
with the problem of distributing data. Various aspects are relevant to
this question if someone is to package data statically (instead of
fetching via some data-sharing framework) into a proper Debian
package:
1. with a
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
well -- this issue is tangentially related to the software: why should
we care about having Debian packages while there are CRAN, easy_install,
etc -- all those great tools to deploy software -- domain specific and
created by specialists. Although such comparison is a stretch, I think
it has its
Le Tue, Feb 15, 2011 at 05:35:07PM -0600, Scott Christley a écrit :
I like the getData effort. Have a set of data descriptors with information
about how/where to get data, then when requested performs the download. This
is very much the architecture I was thinking about. I see a number of
Hi RuiBang,
many thanks for considering to release your bio-medical software under a
free license. While my question rather was about SOAPdenovo because
some colleague had some explicite interest in this part we definitely are
interested in including other high quality software - provided that
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