Re: [RFC] Update libssw? (Needed by parasail)

I'm not against it, as long as it doesn't break any existing packages -- Michael R. Crusoe On Fri, Apr 10, 2020, 00:31 Nilesh Patra wrote: > Hiya, > > The upstream of libssw has version - 1.24 [1] mentioned in their code, and > it seems the haven't made the releases properly. > (This is not the

Re: [RFC] Update libssw? (Needed by parasail)

Hi, The error in parasail complains that some structure doesn't have a `saturated` property. However, the libssw repository you linked to doesn't contain that word either. Thus, the version you deleted has some crucial changes, I guess. There are a few ways you could go. 1) Judging from the name

Re: Some already existing RFP software.

Thanks for taking time for this. Some thoughts I had: For xraylarch I thought maybe this is unique and used for medical imaging and development of medicine. For mapscii I thought maybe this is unique and maybe it could be used for therapeutic treatments. Still it might be interesting for Debi

Re: prinseq(-lite), a dependency of virus seeker

mer...@debian.org, on 2020-04-10 07:04:35 +0300: > Hi Étienne, > > On 2020-04-09 17:16, Étienne Mollier wrote: > > I was trying prinseq-lite with the example files they provided, > > and while prinseq-lite.pl seemed to do its job, there is a side > > script prinseq-graph.pl which calls Statistics:

Re: prinseq(-lite), a dependency of virus seeker

Andreas Tille, on 2020-04-09 23:06:38 +0200: > Hi, > > On Thu, Apr 09, 2020 at 04:59:28PM +0300, Andrius Merkys wrote: > > ... > > I fully subscribe all what Andrius said. :-) > > > Such request to cite is not legally binding. Although it's nice to put the > > citation in debian/upstream/metadat

Re: prinseq(-lite), a dependency of virus seeker

Hi Étienne, On 2020-04-10 11:46, Étienne Mollier wrote: > You're right, assuming the side script is unneeded, this part > may as well wait for after the hackathon. You may drop a TO DO note concerning the side script in debian/TODO file. This way other people may get to know that it is missing an

Re: prinseq(-lite), a dependency of virus seeker

mer...@debian.org, on 2020-04-10 12:15:57 +0300: > On 2020-04-10 11:46, Étienne Mollier wrote: > > You're right, assuming the side script is unneeded, this part > > may as well wait for after the hackathon. > > You may drop a TO DO note concerning the side script in debian/TODO > file. This way ot

Could someone please clarify release status of MUMmer? (Re: Additional info: can not see update note: MUMmer)

Hi, I can not comment on Ben's research. Is there any bioinformatician who could clarify what version of MUMmer should be sensibly packaged? Thanks a lot Andreas. On Fri, Apr 10, 2020 at 08:50:33AM +0200, Ben Tris wrote: > I don't know what it means but the master and develop  v4.0.0beta

Re: Could someone please clarify release status of MUMmer? (Re: Additional info: can not see update note: MUMmer)

Hello, I don't understand that search string, can't make up what exactly was searched on. On the first ten results only this explicitly mentions v4: https://academic.oup.com/gigascience/article/9/2/giaa009/5734639 extra link: https://bioconda.github.io/recipes/mummer4/README.html Nice Day,

Re: Could someone please clarify release status of MUMmer? (Re: Additional info: can not see update note: MUMmer)

Hi All On 10/04/2020 11:31, Andreas Tille wrote: I can not comment on Ben's research. Is there any bioinformatician who could clarify what version of MUMmer should be sensibly packaged? Maybe: as a general guide you should at least provide an equivalent of the most recent bioconda package: h

Bug#956384: ITP: prinseq-lite -- PReprocessing and INformation of SEQuence data (lite version)

Package: wnpp Severity: wishlist Owner: Debian Med Packaging Team * Package name: prinseq-lite Version : 0.20.4 Upstream Author : Robert Schmieder * URL : http://prinseq.sourceforge.net/ * License : GPL-3+ Programming Lang: Perl Description : PReproces

Re: prinseq(-lite), a dependency of virus seeker

Good day, For the record, in addition to the ITP #956384, there is a repository open for prinseq-lite on Salsa: https://salsa.debian.org/med-team/prinseq-lite I'm still playing around inside debian/ to learn how things are put together. Kind Regards, -- Étienne Mollier Fingerprint: 5

Re: [RFC] Update libssw? (Needed by parasail)

Hi Fabian and Micheal On Fri, 10 Apr 2020, 12:35 Fabian Klötzl, wrote: > Hi, > > The error in parasail complains that some structure doesn't have a > `saturated` property. However, the libssw repository you linked to > doesn't contain that word either. Thus, the version you deleted has some > cr

Re: Could someone please clarify release status of MUMmer? (Re: Additional info: can not see update note: MUMmer)

Thanks for finding the mummer4 package, Ben. On 10/04/2020 12:44, Ben Tris wrote: I don't understand that search string, can't make up what exactly was searched on. For the record, that link was to papers citing Kurtz 2004 - in scholar's usual unreadable api style. The https://mummer4.github.

Re: Please choose a free license for gmap

Hi Andreas, It has taken a couple of years, and I don't know if it's relevant any more, but GMAP and GSNAP are now released as open source under the Apache 2.0 license. Thanks, Tom Thomas D. Wu, M.D., Ph.D. Principal Scientist, Bioinformatics & Computational Biology Genentech

Re: Please choose a free license for gmap

Hi Tom, thanks a lot for this helpful hint. Yes, it is definitely relevant. Do you have any link to the source code? Kind regards Andreas. On Fri, Apr 10, 2020 at 10:42:15AM -0700, Thomas Wu wrote: > Hi Andreas, > > It has taken a couple of years, and I don't know if it's relevant any more

Re: Please choose a free license for gmap

All source code is available at http://research-pub.gene.com/gmap The version starting with 2019-12-01 is open source. The most recent version is 2020-04-08. Thanks, Tom Thomas D. Wu, M.D., Ph.D. Principal Scientist, Bioinformatics & Computational Biology Genentech

Re: Fwd: [covid] New Contributor for biohackathon

Hello everybody, I am available to help. I will be working on the TODO list [0]. [0] https://salsa.debian.org/med-team/community/2020-covid19-hackathon/-/wikis/COVID-19-Hackathon-packages-needing-work Cheers, Arias Emmanuel @eamanu yaerobi.com On Fri, Apr 10, 2020 at 3:10 AM Olek Wojnar wrote

Re: prinseq(-lite), a dependency of virus seeker

Hi Étienne, On 2020-04-10 18:54, Étienne Mollier wrote: > For the record, in addition to the ITP #956384, there is a > repository open for prinseq-lite on Salsa: > > https://salsa.debian.org/med-team/prinseq-lite Great job! I have a couple of comments: 1. In Debian it is usual to strip pr