Re: RFS: python3-typed-ast, hisat2

Hi Michael, I took a look at hisat2: - I would add: Copyright 1999, N. Jesper Larsson, all rights reserved. from ls.h to d/copyright - IMHO d/rules should have a ‘clean' override that removes the man pages built there - The watchfile doesn’t have any active entries? The following

CD-HIT binaries (Was: [GSoC] Help needed for verifying cd-hit test)

Hi Andreas, [...] > Is there anybody who would > expect to find a /usr/bin/cdhit executable in any scripts or should we > rather rename to cd-hit to fit the upstream binary. I remember that I had to patch upstream code a couple of times to change the name of the CD-HIT/CD-HIT-EST binaries to

Re: trinityrnaseq in Git

Hi Michael, thanks! Just uploading a fixed version. Cheers and have a nice weekend Sascha > On 5 Aug 2016, at 17:44, Michael Crusoe <michael.cru...@gmail.com> wrote: > > Done, sorry about that! > > [I forced pushed with your commit after mine] > > On Fri, Aug

trinityrnaseq in Git

Hi all, I was going to look at the last GCC 6 FTBFS and trinityrnaseq looks like a good point to start. However, 2.2.0-dfsg-1 is already in unstable but still has UNRELEASED as distribution in Git... if there are any local changes left I would be happy if someone could push them :) Cheers Sascha

Re: mummer patches

Hi Fabian, thanks for the patches! > So I finally got round to submit my patches for MUMmer. One can be found > in the repo, half of the other is attached to this mail. Unfortunately, > the other half got lost in a code reindentation. Applying the changes > requires refactoring

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: linuxbrew with homebrew/science - works!

Hi all, > It features an astonishing array of bioinformatics software and kind of > saves what is left of my sanity to get our local HPC environment going. > Our admins are "its in your home directory" fine with it. Yes, I can see this is one of the main reasons for its popularity, and I also

Re: Sorting our packages into Debian Med or Debian Science tasks

Hi Andreas, > I'm currently running an UDD query to detect not yet categorised > packages[1] of ours and try to put them into tasks that might sound > sensible. Cool, I can also take a look later. > I'm unsure whether we should add libhat-trie-dev to bio-dev > task or some task in Debian

Re: GDPC Autopkgtes [GSOC]

Hi Andreas, […] >> I just pushed my changes to git, maybe it helps. Please note that gdpc is a >> graphical tool; not sure how you would want to do the testing here. >> The current autopkgtests do not segfault anymore, but fail due to X not >> being set up in the testbed. > > Any chance to try

Re: GDPC Autopkgtes [GSOC]

Hi all, >> I'll do report but i am looking at source code of gdpc and can't figure out >> what is wrong i think something about methods is broken. > > Usually injecting some printf("DEBUG %s(%i)", __FILE__, __LINE__) > statements are pretty helpful to detect the location of the problem - > for

Re: Thanks to Gert and Sascha - other please keep on fixing bugs (Was: Thanks to Sascha for his bug fixing - but we should do more (Was: Strengthening team by fixing other members bugs))

>> Mentors list for help which usually receives helpful responses quite >> quickly is invited to work on our bugs. >> >> Kind regards >> >> Andreas. >> >> On Wed, May 04, 2016 at 08:33:08AM +0200, Andreas Tille wrote: >>> >>> Hi, >

Bug#831781: ITP: mash -- fast genome and metagenome distance estimation using MinHash

Package: wnpp Severity: wishlist Owner: Sascha Steinbiss <sa...@debian.org> * Package name: mash Version : 1.1 Upstream Author : Brian Ondov, Todd Treangen, Sergey Koren, and Adam Phillippy <adam.philli...@nih.gov> * URL : https://mash.readthedocs.

Re: A common test-data package for genome assemblers

Hi all, > I've had a couple packages that indicate the availability of data > outside of the source distribution that can be used to try out the > software (and make sure that it actually runs). I didn't think it was a > good idea to bundle the data in with the actual package since it doesn't >

Re: Do you have popularity-contest set to yes?

Hi Andreas, > when looking at our tasks pages I'm noticing several package with 0 > installations reportet. I looked at one of these that looks familiar to me and that I have been tracking in my DDPO for quite a while (Artemis), and DDPO shows 16 installations. Could it be that the tasks pages

rate4site 3.0.0-3 changes

Hi Tanya, while fixing RC bug #811824 [1] I noticed a changelog entry for rate4site 3.0.0-3 by you marked as UNRELEASED. A quick search in the team mailing list didn't turn up anything related to it. I could take a look later if you want and upload (if you think it's ready -- it looks OK to me).

Re: Request for discussion: Is our Sprint more of a Mini-DebConf? What to have next?

Dear Steffen, sorry for my late reply -- I have been busy last week with both work and RL and also had to think a little about your suggestions. [...] >> FYI as a side note: I have reached out to informatics people here at >> Sanger during the regular campus-wide Informatics Group Meetings by >>

Re: Request for discussion: Is our Sprint more of a Mini-DebConf? What to have next?

Hi Steffen and all, > I was peeking into the one or other scientific collaboration of mine to > invite them to our next Debian Med sprint. But I could not really tell > much about it, yet. Besides deciding where to convene next (which to my > recollection is decided by someone saying loudly that

Re: NETTAB 2016 abstract deadline extended to June 30th

Hi all, >> Solicited topics >> http://www.igst.it/nettab/2016/submissions/topics/ >> >> I think a presentation on what Debian (Med) has to offer the >> community would be well received and I would be happy to co-author >> or advise such an abstract. >> >> I plan to submit something there (not

Re: SSPACE (Was: RFS: ariba)

Hi all, [...[ >>> In any case I've updated and pushed what I found on my local disc to Git >>> ... >> >> Yes, I have noticed. Great, thanks! A nice starting point. > > Yup. I would not mind if somebody else would take over (as always ;-)). I have finished SSPACE in git yesterday and it should

Bug#826682: ITP: sspace -- scaffolding pre-assembled contigs after extension

Package: wnpp Severity: wishlist Owner: Sascha Steinbiss <sas...@steinbiss.name> * Package name: sspace Version : 2.1.1 Upstream Author : Marten Boetzer and Walter Pirovano * URL : https://github.com/nsoranzo/sspace_basic * License : GPL-2 Programmin

Help with CMake linking Debian's LLVM libs

Hi, I am trying to make SPAdes 3.8.0 [1] (just entered unstable) build with Debian's packaged LLVM libraries instead of using the version bundled by upstream. I have made the necessary CMake changes [2] in a separate git branch [3] but run into a problem that seems to stem from within the LLVM

Re: solution for testing migration for arch:all package with missing i386 deps

Hi Afif, thanks. I have sent an email and they have put in a hint to force it in; now it’s in testing. Thanks for the help! Cheers Sascha > On 4 Jun 2016, at 07:05, Afif Elghraoui wrote: > > > > على الخميس 2 حزيران 2016 ‫09:47، كتب Afif Elghraoui: >> Here is the thread

plasmidSPAdes tests fail for 3.8.0

Dear SPAdes developer team, while updating the Debian packaging for SPAdes, which also includes adding build-time and installed tests for each tool, I noticed that the plasmidSPAdes tests (plasmidspades.test —test) do not succeed. This consistently happened for the Linux version (tested on

python-csb should now be reproducible

Hi all, I think I have made python-csb reproducible, after making some changes to epydoc which are not yet accepted by the maintainer but already in the r-b custom repo. Could someone please upload so it can run on their Jenkins builders? Thanks Sascha

Re: SSPACE-basic GitHub repository

happy to hear such welcome news and to see good software freed! Best regards Sascha > -- > Nicola Soranzo, Ph.D. > Data Infrastructure & Algorithms group > The Genome Analysis Centre (TGAC) > Norwich Research Park, Norwich, NR4 7UH, UK > http://www.tgac.ac.uk/sequencing-infor

SSPACE-basic GitHub repository

it for Debian. Many thanks Sascha Steinbiss [1] https://github.com/nsoranzo/sspace_basic [2] https://github.com/nsoranzo/sspace_basic/blob/master/COPYING [3] http://www.baseclear.com/genomics/bioinformatics/basetools/SSPACE

python-cobra and rdp-readseq now reproducible

Hi, BTW, the two packages in the subject are now reproducible as well, could someone please take a look? Changes are in git and SVN, respectively. Cheers Sascha -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number

Re: solution for testing migration for arch:all package with missing i386 deps

Hi Andreas, > On Thu, Jun 02, 2016 at 11:45:10AM +0100, Sascha Steinbiss wrote: >> I remember you had recently raised a discussion about circlator not >> being able to migrate to testing because of dependencies missing for >> i386. It now looks like ariba is stuck in

Re: SSPACE (Was: RFS: ariba)

Hi Andreas, >>> OK. I've uploaded ariba to new. >> >> Thanks! Let's hope I will be able to upload updates by myself when it >> hits the archive ;) > > :-) > Otherwise I'd add upload permissions for you ... Well, this was probably the fastest NEW accept I ever witnessed :) So yes, I would like

solution for testing migration for arch:all package with missing i386 deps

Hi Afif, I remember you had recently raised a discussion about circlator not being able to migrate to testing because of dependencies missing for i386. It now looks like ariba is stuck in the same situation [1]. It is also quite likely that this is probably going to be a common problem for any

Re: SSPACE (Was: RFS: ariba)

Hi Andreas, >>> WARNING: sspace not found in path. Looked for >>> SSPACE_Basic_v2.0.pl. But it is optional so will be skipped >>> during assembly >> >> Yes, I have talked to ARIBA upstream (we're conveniently sharing >> the same office) and this is fine to skip; it's not really clear >> whether

Re: RFS: ariba

Duh, missed the link [1] [1] https://anonscm.debian.org/cgit/debian-med/ariba.git S. > On 31 May 2016, at 23:02, Sascha Steinbiss <sas...@steinbiss.name> wrote: > > Hi all, > > ARIBA [1] is ready for sponsoring if anyone can spare some time. It is > lintian

Re: java.util.Properties writer and reproducibility

Hi Emmanuel, many thanks for your reply. > I confirmed that I encountered this issue with the property files > generated by Ant... and I fixed it last week [1] ;) I haven't uploaded > it yet though. Excellent, that was a problem solved quickly :) Thanks you so much. > You are right to be

plast now reproducible

Hi all, see subject, changes are in Git. I have also done some minor fixes (Vcs-*, hardening, …). Cheers, Sascha

java.util.Properties writer and

Hi Emmanuel, sorry for contacting you out of the blue, but I have noticed your kind help for the Debian Med and Reproducible Builds teams before, so I was just going to try my luck again ;) I am currently trying to make king [1] reproducible, which is currently not built reproducibly because

Re: cain and soapdenovo2 now reproducible

Hi Andreas, thanks for the uploads. > On Sat, May 28, 2016 at 12:08:04AM +0100, Sascha Steinbiss wrote: >> new batch of newly reproducible packages: cain and soapdenovo2. I have also >> migrated soapdenovo2 to git and will retire the SVN repo a soon as the >> package is i

cain and soapdenovo2 now reproducible

Hi all, new batch of newly reproducible packages: cain and soapdenovo2. I have also migrated soapdenovo2 to git and will retire the SVN repo a soon as the package is in unstable. Cheers Sascha

Bug#825529: ITP: ariba -- Antibiotic Resistance Identification By Assembly

Package: wnpp Severity: wishlist Owner: Sascha Steinbiss <sas...@steinbiss.name> * Package name: ariba Version : 1.0.0 Upstream Author : Martin Hunt <m...@sanger.ac.uk> * URL : https://github.com/sanger-pathogens/ariba * License : GPL3 Prog

Re: toppred and bowtie now reproducible

Hi Andreas, >>> I've uploaded toppred. >> >> Great, thanks! > > Hope your DD application will proceed so we can stop thanking each > other. ;-) I'm also DAM approved now, so all that's left is account creation :) [...] >> I have changed the corresponding patch in SVN to just set these to >>

Re: toppred and bowtie now reproducible

Hi Andreas, > I've uploaded toppred. Great, thanks! > I've looked at bowtie and I have a question: In the reproducible.patch > you set some varying variables to fixed (basically empty) values in the > Makefile. In addition you are also commenting the variables inside the > code which might

toppred and bowtie now reproducible

Hi all, I’ve made toppred and bowtie reproducible and also did the usual housekeeping (hardening, autopkgtests, …). In git and svn, respectively. Cheers Sascha

Debian Med reproducibility overview

Hi all, FYI: The R-b team now has a list of reproducibility statistics for the packages maintained by the Debian Med team: https://tests.reproducible-builds.org/unstable/amd64/pkg_set_maint_debian-med.html Looking quite good for now, only 50 packages currently unreproducible! Cheers Sascha

Re: SMALT, Bowtie2 and rna-star now reproducible

Hi Afif, > You should be receiving rights to these packages soon so you can handle > the uploads. Excellent, thanks! Have a nice weekend, Sascha > > Thanks and regards > Afif > > على السبت 21 أيار 2016 ‫14:15، كتب Sascha Steinbiss: >> Update: rna-star is no

Re: SMALT, Bowtie2 and rna-star now reproducible

Update: rna-star is now reproducible too, see Git. Cheers Sascha > On 21 May 2016, at 19:21, Sascha Steinbiss <sa...@tetrinetsucht.de> wrote: > > Hi all, > > SMALT and Bowtie2 are now reproducible as well (in Git and Svn, respectively). > Please note that I nee

SMALT and Bowtie2 now reproducible

Hi all, SMALT and Bowtie2 are now reproducible as well (in Git and Svn, respectively). Please note that I needed to make some changes to Bowtie that change its output — in particular, build hostname, time and compiler are no longer recorded at compile time and hence can not be printed in the

T-coffee and wise now reproducible

Dear all, I have made t-coffee and wise reproducible in git, and also did some of the usual housekeeping. If anyone could take a look, please…? Thanks in advance. Cheers Sascha

Re: RFS: ray (now builds reproducibly)

Hi Andreas, > On 18 May 2016, at 23:29, Andreas Tille <andr...@an3as.eu> wrote: > > I'll take it. Greetings from CWL hackathon in Paris, Andreas. Thanks for the upload! All the best wishes to Herve, Michael & Co as well :) Cheers Sascha > > On Wed, May 18, 2016 at

RFS: ray (now builds reproducibly)

Hi all, I have just adjusted ray’s build system in git to make it build reproducibly (and also fixed some more hardening stuff). So if someone wants to do a team upload… Cheers Sascha signature.asc Description: Message signed with OpenPGP using GPGMail

Re: iva_1.0.5-1_amd64.changes ACCEPTED into unstable, unstable

Hi Andreas, > Done. Thanks for your work on this Many thanks to you as well :) > and hope your DD application will be > finalised soon. Yes, I hope so too. Only needs FD and DAM approval now... Cheers Sascha > On Wed, May 11, 2016 at 04:41:52PM +0100, Sascha Steinbiss wrot

Re: iva_1.0.5-1_amd64.changes ACCEPTED into unstable, unstable

ce: iva > Binary: iva > Architecture: source amd64 > Version: 1.0.5-1 > Distribution: unstable > Urgency: low > Maintainer: Debian Med Packaging Team > <debian-med-packag...@lists.alioth.debian.org> > Changed-By: Sascha Steinbiss <sas...@steinbiss.name> > Description:

Re: mypy_0.4-1_source.changes REJECTED

Hi Michael, > FYI, I responded to the activity poll for me Debian Developer > application on April 25th but I haven't heard any reply. Maybe FD haven't processed your reply yet, or there's no AM free at the moment? As my application has been AM approved a week ago, I guess there should be one

Fwd: Re: [Pkg-javascript-devel] New home for datatables.js?

FYI, I have just transferred datatables.js to the Javascript team. Cheers Sascha Forwarded Message Subject: Re: [Pkg-javascript-devel] New home for datatables.js? Date: Fri, 6 May 2016 09:20:05 +0100 From: Sascha Steinbiss <sas...@steinbiss.name> To: Jonas Smedega

Re: RFS: iva

Hi Andreas, > I'll take it. Great, thanks for the upload! Cheers Sascha > > On Thu, May 05, 2016 at 10:58:53AM +0100, Sascha Steinbiss wrote: >> Hi all, >> >> I have found the time to finish packaging of IVA [1]. Could anyone take >> a look please? >> I

RFS: iva

builds reproducibly. Cheers Sascha [1] https://anonscm.debian.org/cgit/debian-med/iva.git -- Dr Sascha Steinbiss Senior Bioinformatician Parasite Genomics Wellcome Trust Sanger Institute Genome Campus, Hinxton, Cambridge, CB10 1SA, UK -- The Wellcome Trust Sanger Institute is operated by Genome

Re: Strengthening team by fixing other members bugs

Hi Andreas, [...] > It would be great if everybody who considers a member of the Debian Med > team (even if not very active until now) would try to fix one bug per > week. Sure, I will see what I can do. How do you propose we as DMs communicate the changes -- just push a new branch in git and

Re: RFS: augustus -- gene prediction in eukaryotic genomes

Hi Afif, thanks for your quick review & reply! […] > where the cd $(CURDIR) lines are unnecessary-- every line in the Make > recipe is called in a fresh shell that will already be in the top-level > directory. True. Changed this to the more idiomatic $(MAKE) -C syntax anyway. > Also, you

RFS: augustus -- gene prediction in eukaryotic genomes

Hi all, I have prepared a version of AUGUSTUS in git. It builds three binary packages: - augustus, with the main binaries - augustus-data, containing pre-built species parameters for the most common organisms, - augustus-doc, which contains documentation such as manual-style READMEs and

Re: Proposal to start link time optimisation for Debian Med packages

Hi Steffen, […] > * minimal impact on regular packaging - maintainers should not need to > worry unless they do want to learn about it. To be achieved by changes > to debhelper and the sharing of our packaging in our source code > repositories. > > * LTO flags should be optionally excluded from

Re: Artemis: fix for #808851

Hi Afif, >> Did I miss something? I have everything to run Artemis (‘java -jar >> /usr/bin/art’ indeed runs Artemis) but the jar wrapper part doesn’t seem to >> work for me. >> > > That's strange. It works for me on jessie. I will take a look, but it > seems as though you don't have

Re: Artemis: fix for #808851

Hi Afif, > > I noticed that Artemis was removed from testing a while ago, and > > one reason was bug #808851. You apparently started to fix it > > (thanks!) but haven't seen an upload for a fixed version, so as I > > had some time to spare this morning I looked at it. I just pushed > > the last

Artemis: fix for #808851

Hi Afif, I noticed that Artemis was removed from testing a while ago, and one reason was bug #808851. You apparently started to fix it (thanks!) but haven't seen an upload for a fixed version, so as I had some time to spare this morning I looked at it. I just pushed the last remaining changes

Re: Request for Sponsoring: spaced

Hi Fabian, > I have prepared a package for spaced (words). The remaining issues are > due to upstream not releasing proper source tarballs (binaries are > included and no versioning). Just a comment about this after taking a quick look: You can directly exclude a binary from the orig tarball

Re: How to convert gb to gbk to get proper input for mauvealigner?

Hi Andreas and Afif, >> a colleague of mine relaised that mauvealigner seems to need gbk files >> when running under Linux (while under Win also gb file is working). This >> happens when using >> >>java -Xmx6g -cp /usr/share/java/Mauve.jar >> org.gel.mauve.contigs.ContigOrderer -output

SILVA replacement pHMMs for Barrnap

Dear Torsten, I hope you are doing well. I was wondering whether you have had a chance to look at my reply to Barrnap issue #13 [1] yet. As discussed last year I have looked into building new profile HMMs from public sources to replace the current ones built from SILVA alignments. I had to remove

Re: Worth packaging bio_assembly_refinement?

Hi Afif, first of all thanks for looking at Circlator, which was on my list as well :) >> I'm looking into packaging Circlator, which depends on the Sanger >> program bio_assembly_refinement. Looking into it, I'm wondering whether >> this is a tool that will just get folded into circlator

Re: [MoM] Outreachy 2016 application

ectory, but rather create a bwa-test package containing the data and make it a dependency of the test. Can anyone perhaps comment on this idea? IMHO you can use test data from other packages, but keep in mind that these can change without warning. Best regards Sascha > 2016-02-23 1:50 GMT+03:00 Sas

Re: Packages for Stable-backports

Hi Afif, > I'm planning to backport several packages for the current stable release > (probably after next week). I wanted to list them here in case there are > any objections or things I should be aware of. They are: > > barrnap > fastaq > roary > tantan > spades Sure, that would be great. For

Re: RFS: reapr

Hi Michael, > Sascha, care to share your reproducibility test setup? Sure, but it’s nothing too flashy and basically just the recommended reference setup. With cowbuilder installed and my pbuilderrc (https://github.com/satta/dotfiles/blob/master/pbuilder/.pbuilderrc) just follow the

biosquid fix for #815883, please review & upload

Hi all, I have prepared a fix for #815883 in SVN and also updated the package to current standards. Could someone sponsor a team upload please? Thanks, Sascha

Re: RFS: reapr

Hey, > [...] >> and builds reproducibly. > > Actually, I just noticed it doesn't! I do get slightly different > binaries (though no timestamps involved) and I can't track it down > further for now. OK, it was just a ccache issue in my reproducibility testing setup. The package is fine!

Re: RFS: reapr

Hi again, [...] > and builds reproducibly. Actually, I just noticed it doesn't! I do get slightly different binaries (though no timestamps involved) and I can't track it down further for now. I'll try to get in touch with the r-b team later. However, I don't consider this an upload blocker at

RFS: reapr

Hi all, with all required dependencies in place now and with a proper test case I think REAPR is ready for upload. Code is in git, could anyone take a look please? The package has no lintian errors/warnings, has build time tests as well as autopkgtests, and builds reproducibly. Many thanks,

Re: [MoM] Outreachy 2016 application

Hi Anna and Andreas, […] >> I got the following error: "Error: container adt-sid-amd64 is not defined" >> >> This discussion >> looks relevant, but the executed command here is slightly different. >> >> Do you have any ideas how to fix

Re: detecting the presence of new files / licenses / copyrights

Hi, > http://sources.debian.net/src/amtterm/1.4-1/debian/rules/?hl=4#L4 > > Has anyone used this technique in practice? Not yet, but it looks useful in case things change. Unfortunately doesn’t help with getting the licenses in to begin with... Thanks for the pointer, Sascha

PBSIM code repository on Google Code

, and if so, if you could consider migrating the code to GitHub? Google Code offers an easy mechanism to do this [3]. Many thanks, Sascha Steinbiss [1] https://code.google.com/archive/p/pbsim/ [2] https://code.google.com/archive/about [3] https://code.google.com/export-to-github/export?project=pbsim

Bug#813385: ITP: reapr -- universal tool for genome assembly evaluation

Package: wnpp Severity: wishlist Owner: Sascha Steinbiss <sa...@tetrinetsucht.de> * Package name: reapr Version : 1.0.18 Upstream Author : Martin Hunt <martin.h...@sanger.ac.uk> * URL : http://www.sanger.ac.uk/science/tools/reapr * License

Bug#812426: ITP: miniasm -- ultrafast de novo assembler for long noisy DNA sequencing reads

Package: wnpp Severity: wishlist Owner: Sascha Steinbiss <sa...@tetrinetsucht.de> * Package name: miniasm Version : 0.2 Upstream Author : Heng Li <l...@me.com> * URL : https://github.com/lh3/miniasm * License : MIT Programming Lang: C

Bug#810600: ITP: minimap -- tool to find approximate mapping positions between long sequences

Package: wnpp Severity: wishlist Owner: Sascha Steinbiss <sa...@tetrinetsucht.de> * Package name: minimap Version : 0.2 Upstream Author : Heng Li <l...@me.com> * URL : https://github.com/lh3/minimap * License : MIT Programming Lang: C

Re: libtabixpp test fixes ready for upload

Hi Andreas, > Uploaded and upload permissions granted for your next package revision. > Thanks for your work on this Thanks for the quick action and the upload permissions. Cheers Sascha

RFS: Roary ready for upload

Dear team, with all Perl dependencies now out of NEW and a crucial bug (#808552) now fixed, Roary is ready for upload in my opinion. Runs its Perl test suite successfully, is lintian clean, and builds reproducibly. Thanks, Sascha

libtabixpp test fixes ready for upload

Hi team, I have fixed autopkgtests in libtabixpp and also moved around dependencies a bit. Could someone upload please? Many thanks, Sascha

Bug#808495: ITP: roary -- high speed stand alone pan genome pipeline

Package: wnpp Severity: wishlist Owner: Sascha Steinbiss <sa...@tetrinetsucht.de> * Package name: roary Version : 3.5.7 Upstream Author : Andrew J. Page <ro...@sanger.ac.uk> * URL : http://sanger-pathogens.github.io/Roary/ * License : GPL-3+ Prog

Bug#807977: ITP: libtabixpp -- C++ wrapper to tabix indexer

Package: wnpp Severity: wishlist Owner: Sascha Steinbiss <sa...@tetrinetsucht.de> * Package name: libtabixpp Version : 1.0.0 Upstream Author : Erik Garrison <erik.garri...@gmail.com> * URL : https://github.com/ekg/tabixpp * License : MIT Program

RFS: snpomatic

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi all, I have prepared snpomatic as a dependency for REAPR (to come). I would be happy if someone could take a look in git. Apart from the missing watch file (no releases tagged by upstream) it is lintian clean and builds reproducibly. Looking

Re: RFS: snpomatic

eading the patch I am happy to oblige ;) > I'd recommend removing these spacing-changing chunks in a next > version of the package. Sure, no problem at all. Thanks for the upload, Sascha > On Mon, Dec 14, 2015 at 03:46:16PM +, Sascha Steinbiss wrote: > Hi all, > > I have

License for tabixpp

Dear Erik, I'm writing you on behalf of the Debian Med team that has the objective to package all Free Software in the field of Biology and Medicine for official Debian. I am currently prepared a Debian package for your Tabix C++ wrapper tabixpp [1]. It is a requirement for other software

Bug#807779: ITP: snpomatic -- fast, stringent short-read mapping software

Package: wnpp Severity: wishlist Owner: Sascha Steinbiss <sa...@tetrinetsucht.de> * Package name: snpomatic Version : 0.0.20151015 Upstream Author : Heinrich Magnus Manske <m...@sanger.ac.uk> * URL : https://github.com/magnusmanske/snpomatic * License

Bug#805693: ITP: codonw -- Correspondence Analysis of Codon Usage

Package: wnpp Severity: wishlist Owner: Sascha Steinbiss <sa...@tetrinetsucht.de> * Package name: codonw Version : 1.4.4 Upstream Author : John Peden <jfp%23hanson-cod...@yahoo.com> * URL : http://codonw.sourceforge.net * License : GPL2 Program

Re: Debmed sprint ?

Hi all, >> Any news regarding next sprint? >> Copenhagen neighbourhood had been suggested, but are a location and date >> fixed? >> >> I d like to look at tickets soon enough to find cheap prices > > See here > > https://wiki.debian.org/Sprints/2016/DebianMed2016 I have just looked at the

RFS: kmc 2.2-1 is ready

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi all, I have updated kmc to the most recent version. Lintian clean in my sid pbuilder. Can someone take a look and upload, please? I would also be happy to get DM permissions, if possible :) Thanks, Sascha -BEGIN PGP SIGNATURE- Version:

Re: DebianMed policy error

Hi, Btw, in the same paragraph, I think it should additionally be '--svn-noautodch' instead of '--svn-no-autodch': [vagrant@debian-8:~] $ svn-buildpackage --help | grep autodch --svn-noautodch Don't add a new Debian changelog entry when done Cheers Sascha On 12/08/2015 10:12, olivier

Re: Hint for newcomers: Please check developers dashboard

Hi all, If you check your developers dashboard https://udd.debian.org/dmd/ you can see all things you could do on packages you touched. […] I’ve actually also found the QA overview very useful, e.g. https://qa.debian.org/developer.php?login=sas...@steinbiss.name which also shows if

Bug#793907: ITP: tantan -- low complexity and tandem repeat masker for biosequences

Package: wnpp Severity: wishlist Owner: Sascha Steinbiss sa...@tetrinetsucht.de * Package name: tantan Version : 13 Upstream Author : Martin Frith tan...@cbrc.jp * URL : http://www.cbrc.jp/tantan/ * License : GPL Programming Lang: C Description : low

Bug#776710: ITP: barrnap-data-nonfree -- non-free pHMMs for barrnap

Package: wnpp Severity: wishlist Owner: Sascha Steinbiss sa...@tetrinetsucht.de * Package name: barrnap-data-nonfree Version : 0.5 Upstream Author : Torsten Seemann torsten.seem...@monash.edu URL : http://www.vicbioinformatics.com/software.barrnap.shtml * License

Re: DebianMed Sprint in St Malo precision

Hi Olivier, By the way, do you think we should work out which rooms to book right now or is it enough just to let them know you are coming now, and group together into rooms when we arrive? Hi, sorry for late answer, you should book it right now. Okay, so if they ask what kind of room I

Re: unstable/experimental freeze policy

On 15/12/2014 11:30, Andreas Tille wrote: Hi Sascha, Hi Andreas, [...] I think by waiting a certain time to see whether some QA tools have run once or twice which is probably in a one month time frame. Oh, I didn't know these tools also run on experimental. In this case I completely agree!

Re: DebianMed Sprint in St Malo precision

Hi Olivier, I have sent an email to the hotel last week to book a room but have not yet received any reply... could it be that they have no network at all right now? By the way, do you think we should work out which rooms to book right now or is it enough just to let them know you are coming

Re: unstable/experimental freeze policy

Hi Andreas, On 16/12/2014 10:08, Andreas Tille wrote: We need to make sure that the *release* has no bugs. If you later upload to unstable and a bug occures you can fix the bug in unstable as usual. But if you have upload to unstable an later a bug in testing is detected you run into

Re: unstable/experimental freeze policy

Hi Andreas, I have just uploaded a new version of a package (new GenomeTools upstream version) to experimental [...] do you see much in the way of uploading this package to unstable as well? You always need to outweight policy with sane reasons / common sense. If you think GenomeTools and

unstable/experimental freeze policy

Hi all, I have a question regarding the jessie freeze policy. In the policy document (https://release.debian.org/jessie/freeze_policy.html) it says that one should keep disruptive changes out of unstable and continue making use of experimental for changes that are not suitable for jessie. I have

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