hing I can do to facilitate this.
>
> Many thanks and regards
> Afif
>
--
Tim Booth <tbo...@ceh.ac.uk>
Centre for Ecology and Hydrology
Maclean Bldg, Benson Lane
Crowmarsh Gifford
Wallingford, England
OX10 8BB
http://environmentalomics.org/bio-linux
+44 1491 69 2297
patches DEP3 headers, and test again.
Le ven. 21 août 2015 14:54, Tim Booth ava...@fastmail.fm a écrit :
I thought that bit was your doing? Maybe I broke it somehow.
All I
intended to do in that package since you worked on it was move
Hi Olivier,
I just added a get-orig-source based on your existing one for sis-base.
I though there might be a good way to watch SVN for new releases but
apparently not.
I don't use svn-buildpackage so didn't see the error there. not sure
what it would be.
Cheers,
TIM
On Fri, 2015-08-21 at
them.
Is it ok for you?
Olivier
--
Tim Booth tbo...@ceh.ac.uk
Centre for Ecology and Hydrology
Maclean Bldg, Benson Lane
Crowmarsh Gifford
Wallingford, England
OX10 8BB
http://environmentalomics.org/bio-linux
+44 1491 69 2297
I thought that bit was your doing? Maybe I broke it somehow. All I
intended to do in that package since you worked on it was move the
libraries into /usr/lib/jni and to remove the .0.0.0 extension. Other
than that I was mainly working on the -jhdf5 package.
TIM
On Fri, 2015-08-21 at 12:37
Hi Olivier,
Following a bit more tinkering with the tests over the last couple of
days, I now have a package for libsis-jhdf5-java that I think is
complete and ready for use with FastQC etc. I have committed all my
work to SVN.
I got sidetracked by the tests in sourceTest/java/test but then I
, Tim Booth wrote:
Hi Olivier,
http://anonscm.debian.org/viewvc/debian-med/trunk/packages/libsis-base-java/
http://anonscm.debian.org/viewvc/debian-med/trunk/packages/libsis-jhdf5-java/
I've not modified FastQC at all. Or rather, I tried patching out the
FAST5 support but I just did
; I'm not
playing with the package from GIT at this point.
Cheers,
TIM
On Fri, 2015-08-14 at 08:16 +0200, olivier.sal...@codeless.fr wrote:
On 08/13/2015 05:20 PM, Tim Booth wrote:
Hi Olivier,
Looks like Bernd Rinn is making positive noises regarding a DFSG version
of the library, so
Hi Charles,
Thanks for the explanation. I can see why this all makes sense so I'll
use the package as it is, once 1.3 comes out.
Cheers,
TIM
On Fri, 2015-08-14 at 07:55 +0900, Charles Plessy wrote:
Le Thu, Aug 13, 2015 at 03:03:34PM +0100, Tim Booth a écrit :
I was looking to see
Hi Charles,
I was looking to see if it was worth pulling the samtools 1.2 package
into Bio-Linux (Ubuntu LTS Backports) and I can see that the package for
1.2 has all the utility scripts going into /usr/bin where before they
were in /usr/{lib,share}/samtools. A slew of Lintian warnings results.
for FAST5 format until we get the library built.
Most users won't need this anyway, and those that do can convert the file
to FASTQ using other tools.
Note you also need to completely remove the file
uk/ac/babraham/FastQC/Sequence/Fast5File.java, which I can't do in a quilt
patch.
Tim Booth - 13th
Hi Andreas and Olivier,
I'm going to have a crack at the FastQC update. I've been poking at the
HDF5 packages and here are my conclusions so far:
---
We have 2 Free Java libraries for HDF5:
1) The NCSA lib distributed by hdfgroup.org with classes in namespace
ncsa.hdf.hdf5lib, packaged on
.
Thanks for your work on this
Andreas.
On Wed, Aug 12, 2015 at 11:44:19AM +0100, Tim Booth wrote:
Hi Andreas and Olivier,
I'm going to have a crack at the FastQC update. I've been poking at the
HDF5 packages and here are my conclusions so far:
---
We have 2 Free Java
Tim,
just for your notice: I injected your source package skbio as
python-skbio to keep name consistency with other Python modules.
Just to make you aware before you might commit skbio yourself.
Kind regards
Andreas.
--
Tim Booth tbo...@ceh.ac.uk
Centre for Ecology
hopefully I am equipped to make sense of the testing problems.
Cheers,
TIM
On Wed, 2015-07-29 at 16:51 +0200, Andreas Tille wrote:
On Wed, Jul 29, 2015 at 03:24:39PM +0100, Tim Booth wrote:
Furthermore, burrito needs the python-future library from here:
https://github.com/PythonCharmers
other tools.
This package was prepared by Tim Booth for BioLinux to update the qiime
package. It is taken over into the Debian Med team and will be maintained
at
git://anonscm.debian.org/debian-med/ea-utils.git
___
Debian-med-packaging
you volunteer to commit your packaging to VCS to let me continue from
there?
Kind regards
Andreas.
[1] https://github.com/najoshi/sickle/releases
--
Tim Booth tbo...@ceh.ac.uk
Centre for Ecology and Hydrology
Maclean Bldg, Benson Lane
Crowmarsh Gifford
Wallingford, England
-java/trunk/
[4] http://sk-3.tbm.tudelft.nl/dsol/1.6/dsol/source-repository.html
[5] http://sourceforge.net/projects/dsol/files/dsol/dsol-1.6/
[6] http://sourceforge.net/projects/dsol/files/dsol/dsol-2.1.0/
--
Tim Booth tbo...@ceh.ac.uk
NERC Environmental Bioinformatics Centre
Centre
.
--
http://fam-tille.de
--
Tim Booth tbo...@ceh.ac.uk
NERC Environmental Bioinformatics Centre
Centre for Ecology and Hydrology
Maclean Bldg, Benson Lane
Crowmarsh Gifford
Wallingford, England
OX10 8BB
http://environmentalomics.org/bio-linux
+44 1491 69 2297
--
Tim Booth tbo
, 2015 at 06:08:49PM +, Tim Booth wrote:
It's great to hear that you are using Bio-Linux and want to contribute
your Bpipe package. We also have a need for an effective lightweight
pipeline system that supports clusters and doesn't rely on a web client
(Galaxy) or a mountain of Java
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NERC Environmental
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Tim Booth tbo...@ceh.ac.uk
NERC Environmental Bioinformatics Centre
Centre for Ecology and Hydrology
Maclean Bldg, Benson Lane
Crowmarsh Gifford
Wallingford, England
OX10 8BB
http://nebc.nerc.ac.uk
+44 1491 69 2705
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basis.
Kind regards
Andreas.
[1] svn://anonscm.debian.org/debian-med/trunk/packages/cytoscape/trunk/
[2] https://github.com/cytoscape
--
Tim Booth tbo...@ceh.ac.uk
NERC Environmental Bioinformatics Centre
Centre for Ecology and Hydrology
Maclean Bldg, Benson Lane
Crowmarsh
dotur. Upstream does recommend
to use mothur instead. Please raise your hand if you keep on using
dotur for whatever reason or it will be removed from Debian.
Kind regards
Andreas.
--
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NERC Environmental Bioinformatics Centre
Centre for Ecology
...@tetrinetsucht.de
An: Tony Travis tony.tra...@minke-informatics.co.uk,
olivier.sal...@codeless.fr olivier.sal...@codeless.fr, Tim Booth
tbo...@ceh.ac.uk, Debian Med Project List debian-med@lists.debian.org
Betreff: Re: Next sprint proposal
On 09.02.2014 16:50, Tony Travis wrote:
On 09/02/14 15:50
: Tim Booth tbo...@ceh.ac.uk
To: helpd...@nebc.nerc.ac.uk helpd...@nebc.nerc.ac.uk
Subject: RE: [NEBC-NBAF #14791] Staden package-gap5
Date: Mon, 27 Jan 2014 14:05:41 +
Dear Jan,
Thanks for the comments. I'll leave it to Andreas but I suspect he'll
stick with the wrapper scheme I described
is it not in the tarball? My quick guess is that anfo.1 should
be in the tarball and anfo-sge.1 should be absent and the auther just
screwed up making the tarball. A little more detective work needed...
Cheers,
TIM
--
http://fam-tille.de
--
Tim Booth tbo...@ceh.ac.uk
NERC Environmental Bioinformatics
replacements.
Kind regards and thanks for your initial work on this
Andreas.
--
Tim Booth tbo...@ceh.ac.uk
NERC Environmental Bioinformatics Centre
Centre for Ecology and Hydrology
Maclean Bldg, Benson Lane
Crowmarsh Gifford
Wallingford, England
OX10 8BB
http://nebc.nerc.ac.uk
+44 1491
. Please ping me whether I should
take over (like issuing ITP and uploading to Debian) if you consider
this package ready.
Kind regards and many thanks for your commits which are really helpful
to keep on the proper speed inside Debian with the BioLinux related
packages
Andreas.
--
Tim
...
actually, these index files are pretty small. I'll just generate them
at build time and put them in the .deb. Much simpler than messing with
postinst. Will push patches to SVN shortly.
TIM
On Wed, 2013-06-05 at 12:27 +0100, Tim Booth wrote:
Hi Andreas,
I spoke too soon
about such
package will notice the BioLinux string and might become interested in
it ...
Kind regards
Andreas.
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Tim Booth tbo...@ceh.ac.uk
NERC Environmental Bioinformatics Centre
Centre for Ecology and Hydrology
Maclean Bldg, Benson Lane
Crowmarsh Gifford
Wallingford, England
it now.
Cheers,
TIM
--
Tim Booth tbo...@ceh.ac.uk
NERC Environmental Bioinformatics Centre
Centre for Ecology and Hydrology
Maclean Bldg, Benson Lane
Crowmarsh Gifford
Wallingford, England
OX10 8BB
http://nebc.nerc.ac.uk
+44 1491 69 2705
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wrote:
Hi Tim,
On Mon, Jun 03, 2013 at 04:53:03PM +0100, Tim Booth wrote:
This would be nice to get into Debian proper. Even though the upstream
is not being updated the use of ChimeraSlayer seems to be important in
many analysis protocols aside from being wanted by QIIME.
BTW, I have
, not an updated bowtie.
But I'm not doing that today - I'm off to the Gym instead ;-)
Cheers,
TIM
--
Tim Booth tbo...@ceh.ac.uk
NERC Environmental Bioinformatics Centre
Centre for Ecology and Hydrology
Maclean Bldg, Benson Lane
Crowmarsh Gifford
Wallingford, England
OX10 8BB
http
Hi,
The treeviewx package is totally broken (on Ubuntu at least) due to a
longstanding bug. A patch was just submitted by a contributor on Google
code so I've checked it and added it to the package in SVN.
I don't know if there is a corresponding Debian bug, but there are bug
reports in both
Hi Charles,
I'll be up at the EBI in a couple of weeks. Is there anything I can do
to try and persuade them to grant an acceptable license or has this
already been tried? EMBOSS is a software package that I still consider
to be very important, even though development is currently stalled due
to
talk slides to the Wiki - if the other speakers would
like to share their slides then please add your link directly to the
page.
http://wiki.debian.org/DebianMed/Meeting/Southport2012
Cheers,
TIM
On Fri, 2012-01-20 at 18:24 +, Tim Booth wrote:
Dear All,
This is probably the final
Hi Andreas,
11) License checking
I was suggesting an ePetition to free Phylip and wrote a first draft
for it[6]
I put my name to this already and also fixed a couple of typos in the
text.
Since you said this is a draft I also made some changes - take them or
revert them as you
Hi Andreas,
I've been taking a look at ARB just now, and I see you've done a heck of
a lot of work on it. I have a couple of questions that I can't find
answers for in the changelog or README.source, so hopefully you can
help.
1) Do you know what is keeping ARB in non-free apart from the
on working on that myself.
Once I have something working I'll bung it in SVN (hopefully this
afternoon). I'm calling the package 'libhmsbeagle1' as there is already
a beagle package and this is the internal name of the library.
Cheers,
TIM
--
Tim Booth tbo...@ceh.ac.uk
NERC Environmental
Hi,
An update on this:
1) I do have a real user who raised the speed issue doing real analysis
but admitted his script was both unusual and poorly written (aligning
short sequences one at a time).
2) For Bio-Linux users I'm now providing ncbi-blast+-static as an
optional drop-in replacement for
, maybe ...
Maybe, but anyone assembling HT sequence isn't going to care about
saving 120K of space so I think there may be better uses for your
time ;-)
Cheers,
TIM
--
Tim Booth tbo...@ceh.ac.uk
NERC Environmental Bioinformatics Centre
Centre for Ecology and Hydrology
Maclean Bldg, Benson Lane
Hi All,
Following the very successful Debian Med Bioinformatics Sprint last year
in Luebeck, we propose a second one to be held in the UK early next
year. As I didn't duck fast enough I'm currently the main organiser.
The likely location is Southport (exact venue TBC) on the north west
coast of
a speed
comparison with the binary version distributed by NCBI. I'll try that
today.
Cheers,
TIM
Olivier
Le 8/2/11 6:53 PM, Tim Booth a écrit :
Hi Olivier and Aaron,
I've been playing around with BLAST+, trying to tackle one fairly simple
but unimportant issue and one more complex
Hi Olivier and Aaron,
I've been playing around with BLAST+, trying to tackle one fairly simple
but unimportant issue and one more complex and problematic issue.
The easy one first:
In the build log (on Launchpad) I see that during the test phase of the
build there are various attempts to
Hi Olivier,
I'm having a look at the package now. I've pushed some changes to SVN
already - I hope you don't mind. To explain...
I don't think you need to repack the source in this case. The
guidelines say to rename the tarball file, but not to change the
contents unless there is a pressing
Hi Olivier,
This was on my RADAR but I'm currently about to tackle AmplicoNoise
(must remember to file an ITP before I start...) so please go ahead. I
had a look at it at the sprint and this is what I found:
1) This may have been down to our rubbish wireless link but there
appeared to be
Hi,
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. My
understanding is that a Debian Developer should OK the package and file
an ITP so that nobody else starts on their own version. Is that right?
Also, who edits
as you suggested.
Now back to microbiomeutil.
Cheers,
TIM
On Sat, 2011-04-09 at 12:23 +0900, Charles Plessy wrote:
Le Fri, Apr 08, 2011 at 06:20:01PM +0100, Tim Booth a écrit :
1) If I build the package with 'fakeroot debian/rules binary-arch' it
works fine. If I build with 'debuild
Hi,
I'm pushing my changes to cdbfasta to SVN. I'm packaging this because
it is needed for chimeraslayer (part of microbiomeutil). I'm packaging
chimeraslayer because it's needed by qiime.
Steffen had made a start but the package in SVN was just a stub. I'm
pretty well done but I'm stumped on
Hi Steffen,
I've pushed some modifications to the Qiime package - I'm not finished
yet as it doesn't work properly but you can see what I'm doing. Apart
from various cleanups (eg. original package ended up with two copies of
the documentations and various files erroneously gzipped) my main
Some answers on BLAST+ and T-Coffee...
along with BLAST+
enables a key mode of operation in T-Coffee but currently the BLAST+ bit
only works with our bio-linux-blast+ package. I'm continuing to work on
this.
Did you actually found out what BLAST+ is (I remember you were wondering
Hi,
the tm-align package would be ready for upload if somebody would care
for a manpage to TMscore. I have not found any good docs which would
enable me writing it. The help2man workaround results in a poor manpage
without a good usage guideline. Any volunteers?
My favoured way of doing
,
TIM
--
Tim Booth tbo...@ceh.ac.uk
NERC Environmental Bioinformatics Centre
Centre for Ecology and Hydrology
Maclean Bldg, Benson Lane
Crowmarsh Gifford
Wallingford, England
OX10 8BB
+44 1491 69 2705
--
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is subject
,
Tim Booth
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