Hi German,
I'm writing you on behalf of the Debian Med team which tries to include
all free software which is relevant for medicine and biology into main
Debian. If you want to have a look onto our work you might like to look
onto our so called tasks Biology[1] and Biology Developmen[2].
I stumb
Hi Andreas,
Thanks for your interest in SMALT. I have cleaned up the test routines
for the installation/distribution somewhat with the latest release 0.7.6
which you can download from smalt.sourceforge.net.
1. Since we always want to honour scientist work we would like to
add some citat
Hi Hannes,
many thanks for your quick response.
On Tue, Apr 08, 2014 at 04:07:24PM +0100, Hannes Ponstingl wrote:
> Thanks for your interest in SMALT. I have cleaned up the test
> routines for the installation/distribution somewhat with the latest
> release 0.7.6 which you can download from smalt
Hi Andreas,
There is no dependency on BioPython. The 'from formats import Cigar'
line imports the class Cigar from the Python module
smalt/test/formats.py which should be part of the distribution.
For output in the binary format BAM and input from BAM/SAM files (see
samtools.sourceforge.net)
[Metaquestion: Usually we do all discussion in public on our
mailing list. Would you give me permission to forward our
conversation to the list?]
Hi again,
I made some step forward with the tests (see below)
On Tue, Apr 08, 2014 at 07:38:54PM +0200, Andreas Tille wrote:
> ERROR when mapping:
Hi Andreas,
Fine with me if you would like to forward our conversation to the list.
The attached patch should fix the glitch with the dependencies of
bam_cigar_test.py you correctly identified.
Perhaps I should try and package smalt myself but I have no experience
with this and currently not m
Hi Hannes,
On Wed, Apr 09, 2014 at 09:40:14AM +0100, Hannes Ponstingl wrote:
> There is no dependency on BioPython. The 'from formats import Cigar'
> line imports the class Cigar from the Python module
> smalt/test/formats.py which should be part of the distribution.
OK, I found the issue since m
Hi Hannes,
On Wed, Apr 09, 2014 at 10:06:18AM +0100, Hannes Ponstingl wrote:
> Hi Andreas,
>
> Fine with me if you would like to forward our conversation to the list.
Done. Thanks for the permission.
> The attached patch should fix the glitch with the dependencies of
> bam_cigar_test.py you co
Hello,
over the last days I had surprised myself with the fun I had
while following Charles' download and post-process instructions
for the complete genomes.
To help the cleanliness of the getData Perl script, Charles
came up with the idea to have Makefiles share a good part of
the functionality
Hello,
bowtie2 has stuck in unstable because of change in supported architectures.
I've opened #742614, but haven't received any reaction so far.
Is there anything else one can do to force the transition ?
Thank you,
Alex
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with a
Hi,
On Wed, Apr 09, 2014 at 05:42:22PM +0200, Alex Mestiashvili wrote:
> bowtie2 has stuck in unstable because of change in supported architectures.
> I've opened #742614, but haven't received any reaction so far.
>
> Is there anything else one can do to force the transition ?
May be also pingin
On Wed, 9 Apr 2014, Andreas Tille wrote:
On Wed, Apr 09, 2014 at 05:42:22PM +0200, Alex Mestiashvili wrote:
bowtie2 has stuck in unstable because of change in supported architectures.
I've opened #742614, but haven't received any reaction so far.
Is there anything else one can do to force the
Hi Thorsten,
On Wed, Apr 09, 2014 at 10:18:02PM +0200, Thorsten Alteholz wrote:
> >
> >May be also pinging "our" ftpmaster assistant? ;-)
>
> Hmm, sorry, but I don't do rm's. They are far too exciting for my
> poor heart.
:-)
> But you might ask on #debian-ftp for a more robust person ...
I wa
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