done in Debian Med team and is available at
> > Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/cdbfasta/trunk/
> >
> >
> > --
> > To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org
> > with a subject of "unsubscribe". Trouble? Cont
ould be packages specifically as
"bowtie2", not an updated "bowtie".
But I'm not doing that today - I'm off to the Gym instead ;-)
Cheers,
TIM
--
Tim Booth
NERC Environmental Bioinformatics Centre
Centre for Ecology and Hydrology
Maclean Bldg, Benson Lane
Crowm
...
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 spo
versioning:
>
> ~biolinux- or
> -0biolinux
>
> A positive side effect is that people who stumbly by chance about such
> package will notice the BioLinux string and might become interested in
> it ...
>
> Kind regards
>
> Andreas.
>
--
Tim B
ning system so no point trying to second guess it now.
Cheers,
TIM
--
Tim Booth
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
--
To UNSUBSCRIBE, emai
ke sense?
Cheers,
TIM
On Tue, 2013-06-04 at 11:57 +0200, Andreas Tille 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 Chime
with that and push progress to SVN.
I can't recall if there is an ITP for that but I'll check.
Cheers,
TIM
On Tue, 2013-06-04 at 14:51 +0200, Andreas Tille wrote:
> Hi Tim,
>
> On Tue, Jun 04, 2013 at 12:38:45PM +0100, Tim Booth wrote:
> > I've pushed a tiny fix to
ch are really helpful
> to keep on the proper speed inside Debian with the BioLinux related
> packages
>
> Andreas.
>
--
Tim Booth
NERC Environmental Bioinformatics Centre
Centre for Ecology and Hydrology
Maclean Bldg, Benson Lane
Crowmarsh Gifford
Wallingford, England
OX10 8
r* b = 0 )
>^
> make[4]: *** [align.lo] Error 1
>
>
> I wonder whether the package is worth spending more time into it (asking
> some C++ experts what might be wrong here) or whether the package might
> be not needed any more since there might be some better replacements.
&
efinitely not the
one. And the right manpage is actually there in the GIT repo:
https://github.com/udo-stenzel/anfo/tree/master/man
So why 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
e ----
From: Tim Booth
To: 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, as this is the
on: "Sascha Steinbiss"
> > An: "Tony Travis" ,
> > "olivier.sal...@codeless.fr" , "Tim Booth"
> > , "Debian Med Project List"
> > Betreff: Re: Next sprint proposal
> >
> > On 09.02.2014 16:50, Tony Travis wrote:
opinions about 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.
--
Tim Booth
NERC Environmental Bioinformatics Centre
in BioLinux if you could
> commit it into Debian Med SVN to work on a common basis.
>
> Kind regards
>
> Andreas.
>
> [1] svn://anonscm.debian.org/debian-med/trunk/packages/cytoscape/trunk/
> [2] https://github.com/cytoscape
>
--
Tim Booth
NERC Environment
; Do not hesitate to contact me.
>
>
> [0] https://wiki.debian.org/Sprints/2015/DebianMed2015
>
>
> Olivier
>
>
--
Tim Booth
NERC Environmental Bioinformatics Centre
Centre for Ecology and Hydrology
Maclean Bldg, Benson Lane
Crowmarsh Gifford
Wallingford,
sy to add.
>
> Many thanks,
>
> Simon Sadedin
> Murdoch Childrens Research Institute
> Bioinformatics
>
> __
> This email has been scanned by the Symantec Email Security.cloud service.
> For more information please visit htt
t; On 6/02/2015 7:51 am, "Andreas Tille" wrote:
>
> >Hi Simon,
> >
> >I'm writing you as a member of the Debian Med team.
> >
> >On Thu, Feb 05, 2015 at 06:08:49PM +, Tim Booth wrote:
> >> It's great to hear that you are using Bio-L
he source package of your experiment to
> enable me understanding / reproducing what you really did. I could
> continue with testing the reverse dependencies. I simply want to
> push this forward even with my limited skills.
>
> Kind regards
>
>Andreas.
>
> --
&g
> [1]
> https://lists.alioth.debian.org/pipermail/debian-med-packaging/2015-March/031703.html
> [2] https://lists.debian.org/debian-med/2015/03/msg00066.html
> [3] svn://anonscm.debian.org/debian-med/trunk/packages/libdsol1-java/trunk/
> [4] http://sk-3.tbm.tudelft.nl/dsol/1.6/dsol/source-
nd I would like to update the package. Would
> 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
Centre for Ecology and Hydrology
e
> automatic benchmarking and tuning. It uses the same "squared distance for
> anchored alignment" as other tools.
> * varcall
> Takes a pileup and calculates variants in a more easily parameterized manner
> than some other tools.
>
>
> This package was prepare
bugging so
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:
> >
at 17:08 +0200, Andreas Tille wrote:
> Hi 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
>
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 De
#x27;ll be available vor sponsering as usual.
>
> 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
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.
>>PATCH for FASTQC
This patch disables support 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.jav
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 :
> >
> >
ource; 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 r
at 17:20 +0200, olivier.sal...@codeless.fr wrote:
> On 08/14/2015 10:48 AM, 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-j
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
re
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 1
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 +000
d/source and
> updates patches DEP3 headers, and test again.
>
>
> Le ven. 21 août 2015 14:54, Tim Booth 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
&
and check for cleanup.
> 4) when both have moved to git, I upload them.
>
>
> Is it ok for you?
>
>
> Olivier
--
Tim Booth
Centre for Ecology and Hydrology
Maclean Bldg, Benson Lane
Crowmarsh Gifford
Wallingford, England
OX10 8BB
http://environmentalomics.org/bio-linux
+44 1491 69 2297
Please let me know if there's anything I can do to facilitate this.
>
> Many thanks and regards
> Afif
>
--
Tim Booth
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
--
Of course I'm a technophobe; I program computers for a living!
--
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with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org
Archive:
http://lists.debian.org/129641050
y liked having the hacking right in
the hotel though so maybe we should stick with out-of-season coastal
towns that have rail links and find a similar hotel again. Southend?
Bognor Regis? Weston-super-Mare? Walton on the Naze? What do my
fellow Brits think?
Cheers,
TIM
--
Tim Booth
NERC Envir
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 wonde
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 doin
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 change
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
ation 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&#
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 somethi
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 t
Hi,
I'd not thought about this. The ampliconnoise.1 is generated from the
ampliconnoise.pod which was hand written by me, so that's OK.
The Doc.pdf is presumably made from a Word document that is in the
possession of Chris Quince. I'm sure he'd be prepared to send a copy
and even put it in the
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 re
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 connect
version from source in order to do 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 aroun
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
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
the documentation into python-pynast-doc.
> It is not so large and the tool is not used in constrained
> environments ... well, clouds, 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 ;-)
Ch
w get your name on the Wiki list. And in
particular please contribute to the discussion regarding the themes and
aims of this meeting, which we can now start in earnest.
Cheers,
TIM
--
Tim Booth
NERC Environmental Bioinformatics Centre
Centre for Ecology and Hydrology
Maclean Bldg, Benson
Hi Andreas,
> I wanted to address #639389 by using dh --with python2 and dropping
> python-central because neither the current Debian package nor your
> packaging in branch builds under unstable.
OK.
> When inspecting the
> packaging you are keeping in branch I noticed that you forget committi
7;t planning 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
NERC
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 depence
Hi again,
OK - I just found
http://lists.debian.org/debian-devel/2009/05/msg00679.html
Might be worth noting this within README.source.
Cheers,
TIM
On Fri, 2012-01-06 at 16:43 +, Tim Booth wrote:
> Hi Andreas,
>
> I've been taking a look at ARB just now, and I see you
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 like
linked my 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
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
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 Lau
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