Re: [GSoC] any success with ncbi-blast+?

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.

Re: Links to Debian packages

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

Re: New version of ncbi-blast+ available

- 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

Re: New version of ncbi-blast+ available

- 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

Links to Debian packages

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

Re: New version of ncbi-blast+ available

- 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

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 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

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 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

Please provide source code for MALT

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

Re: Description for lefse tools (Was: Origin of data files in MetaPhLan2)

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.

Re: Status of seqan

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: > >

Re: Description for lefse tools (Was: Origin of data files in MetaPhLan2)

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

Re: [ncbi-blast+] 01/01: upload upstream release 2.3.0

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

Re: Status of seqan

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

Re: [ncbi-blast+] 01/01: upload upstream release 2.3.0

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

[ti...@debian.org: Bug#833388: ITP: metaphlan2 -- Metagenomic Phylogenetic Analysis]

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:

Re: [ncbi-blast+] 01/01: upload upstream release 2.3.0

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

Re: [ncbi-blast+] 01/01: upload upstream release 2.3.0

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

Re: [ncbi-blast+] 01/01: upload upstream release 2.3.0

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

Re: Status of seqan2

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

Re: Description for lefse tools (Was: Origin of data files in MetaPhLan2)

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

Re: Description for lefse tools (Was: Origin of data files in MetaPhLan2)

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

Re: Please provide source code for MALT

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

[GSoC] ncbi-blast+ and htslib uploaded

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, ->