Hi Nicola,
On Wed, Aug 03, 2016 at 08:51:33PM +, Nicola Segata wrote:
> Great, thanks Andreas. We provide the "*.bt2" files so that the user can
> run BowTie2 internally to MetaPhlAn directly without first building the
> indexes (it will take quite a bit of time).
Fully agreed here.
> Also,
Great, thanks Andreas. We provide the "*.bt2" files so that the user can
run BowTie2 internally to MetaPhlAn directly without first building the
indexes (it will take quite a bit of time). Also, the indexes are smaller
in size than the sequence file...
cheers
Nicola
On Wed, Aug 3, 2016 at 6:08 PM
Please join the discussion on debian-devel (see below). Andreas.
- Forwarded message from Andreas Tille -
Date: Wed, 03 Aug 2016 21:00:05 +0200
From: Andreas Tille
To: Debian Bug Tracking System
Subject: Bug#833388: ITP: metaphlan2 -- Metagenomic Phylogenetic Analysis
X-Debian-PR-Mess
Thank you!
Le mer. 3 août 2016 à 21:37, Aaron M. Ucko a écrit :
> olivier sallou writes:
>
> > you did not pushed your updates with new upstream release?
>
> I asked about that earlier; he said that he had been concerned that he
> might have incorrectly refreshed the existing patches.
>
> At an
Hi Sascha,
On Wed, Aug 03, 2016 at 05:15:15PM +0100, Sascha Steinbiss wrote:
> > is it correct to assume that packaging seqan2 version 2.2 instead of 2.1
> > is the right way to go and should I help doing so?
>
> Well, if I could make a wish, then I would say 2.2 for sure! I have a
> half-ready p
olivier sallou writes:
> you did not pushed your updates with new upstream release?
I asked about that earlier; he said that he had been concerned that he
might have incorrectly refreshed the existing patches.
At any rate, I'm on it, and should be able to upload 2.4.0 tonight.
For the record,
On Wed, Aug 03, 2016 at 06:35:53PM +, olivier sallou wrote:
>
> oh sorry, I just saw an unpackaged release in changelog and though it is
> the expected one.
>
> you did not pushed your updates with new upstream release?
Yes, I did not pushed as I tried to explain to Aaron since I'm not full
Le mer. 3 août 2016 à 20:06, Andreas Tille a écrit :
> Olivier, your @d.o address was bouncing - so I tryy the list.
>
> Your upload was of the old version instead of the new version 2.4.0
> which should be packaged.
>
oh sorry, I just saw an unpackaged release in changelog and though it is
the
Olivier, your @d.o address was bouncing - so I tryy the list.
Your upload was of the old version instead of the new version 2.4.0
which should be packaged.
Kind regards
Andreas.
- Forwarded message from Andreas Tille -
Date: Wed, 3 Aug 2016 18:10:40 +0200
From: Andreas Tille
Hi Andreas,
> is it correct to assume that packaging seqan2 version 2.2 instead of 2.1
> is the right way to go and should I help doing so?
Well, if I could make a wish, then I would say 2.2 for sure! I have a
half-ready package for the free fast BLAST replacement Lambda [1] and
upstream states t
Hi Tin,
On Wed, Aug 03, 2016 at 02:01:01PM +, Duy Tin Truong wrote:
> > - Tin can also provide more info about the binary data in db_v20. The files
> > ending with "bt2" are created using a script in the Bowtie2 package
> > (bowtie2-build) using a sequence file Tin can provide (it can also be
Hi again,
is it correct to assume that packaging seqan2 version 2.2 instead of 2.1
is the right way to go and should I help doing so?
Kind regards
Andreas.
On Tue, Aug 02, 2016 at 09:10:27AM +0200, Andreas Tille wrote:
> On Thu, Jul 21, 2016 at 12:52:54PM +1000, Kevin Murray wrote:
> >
>
Hi Andreas,
Thanks for you work. I answer your questions as bellow:
- some small fixes:
https://anonscm.debian.org/viewvc/debian-med/trunk/packages/metaphlan2/trunk/debian/patches/fix_sequence.patch?view=markup
-> fixed
- some spelling issues https://anonscm.debian.
org/viewvc/debian-med/tru
Hi Jihyeok,
thanks a lot for this effort. Just for to let the list know: I've
created a Wiki page for this kind of efforts to keep track since
otherwise I might forget to nag again. Feel free to add other
liberation attempts here:
https://wiki.debian.org/DebianMed/SoftwareLiberation
Kind r
Hi Nicola,
thanks for your answer.
On Tue, Aug 02, 2016 at 04:32:31PM +, Nicola Segata wrote:
> Hi Andreas,
> sorry for the delay in replying. I did get your last two emails but it
> seems the fist one (On Mon, Jul 25, 2016 at 09:45:57PM) never arrived.
Hmmm, sad that there seems to be some
Hi Canberk,
On Wed, Aug 03, 2016 at 11:40:58AM +0300, Canberk Koç wrote:
> I prepare htslib and commit.
I uploaded htslib and Olivier cared for ncbi-blast+
Suggested todo list
ncbi-tools6
njplot (according to manual there is an option without X11,
-> https://ano
Dear Prof. Dr. Daniel Huson,
I’m writing to you on behalf of the Debian Med team which is a subgroup inside
Debian with the objective to package free software in the field of biology and
medicine. You can see the packages we worked on in the field of bioinformatics
on our so-called tasks list[1
- Mail original -
> De: "Andreas Tille"
> À: "Olivier Sallou"
> Cc: debian-med@lists.debian.org
> Envoyé: Mercredi 3 Août 2016 11:25:57
> Objet: Re: New version of ncbi-blast+ available
>
> On Wed, Aug 03, 2016 at 11:09:17AM +0200, Olivier Sallou wrote:
> > > Great. May be I simply me
On Wed, Aug 03, 2016 at 11:09:17AM +0200, Olivier Sallou wrote:
> > Great. May be I simply messed up the patches. Could you push (or even
> > upload - may be after running the autopkgtest)?
>
> autopkgtest si not automatically ran during build ?
No, its no build time test (may be its a good ide
- Mail original -
> De: "Andreas Tille"
> À: debian-med@lists.debian.org
> Envoyé: Mercredi 3 Août 2016 11:00:51
> Objet: Re: New version of ncbi-blast+ available
>
> On Wed, Aug 03, 2016 at 10:42:14AM +0200, Olivier Sallou wrote:
> > > I just imported the new tarball and tried to refre
On Wed, Aug 03, 2016 at 10:42:14AM +0200, Olivier Sallou wrote:
> > I just imported the new tarball and tried to refresh the patches. Some
> > small adaptions were needed but I'd prefer you do these with a deeper
> > understanding. I became unsure whether I might have mixed up with the
> > wrong
- Mail original -
> De: "Andreas Tille"
> À: debian-med@lists.debian.org
> Cc: "Aaron M. Ucko"
> Envoyé: Mardi 2 Août 2016 22:54:16
> Objet: Re: New version of ncbi-blast+ available
>
> Hi Aaron,
>
> On Tue, Aug 02, 2016 at 04:03:48PM -0400, Aaron M. Ucko wrote:
> > > I gonna have a l
On Wed, Aug 03, 2016 at 07:55:03AM +0200, Andreas Tille wrote:
> Hi Canberk,
>
> On Wed, Aug 03, 2016 at 01:35:39AM +0300, Canberk Koç wrote:
> >
> > I prepare amap-align but package not in git can you please move it to git.
>
> I'll do - could you meanwhile pick another package from the list.
Hi Jon,
On Wed, Aug 03, 2016 at 09:23:07AM +0200, ji...@cbs.dtu.dk wrote:
> Forgive the very naive question, but do you maintain a list of links to
> packages (source, binary) currently available in
> the Debian distro ?
>
> I want to support linking to Debian packages from named tools in bio.to
Hi folks
Forgive the very naive question, but do you maintain a list of links to
packages (source, binary) currently available in
the Debian distro ?
I want to support linking to Debian packages from named tools in bio.tools.
If not a link, I guess I could just support package names; in this ca
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