Re: What is the relation ncbi-magicblast and magicblast

2020-06-20 Thread Andreas Tille
Hi Aaron, On Fri, Jun 19, 2020 at 12:09:56PM -0400, Aaron M. Ucko wrote: > Declaring a build dependency on the time package clears up these > immediate errors. However, several tests involve connecting to the > network, and blast_services_unit_test fails even when it can connect, I > think due to

Re: Bug#963052: ITP: pairtools -- Framework to process sequencing data from a Hi-C experiment

2020-06-20 Thread Andreas Tille
On Fri, Jun 19, 2020 at 09:18:05PM +, Antoni Villalonga wrote: > Hi, > > pairtools is getting closser to be ready. > > https://salsa.debian.org/med-team/pairtools Uploaded and added to https://salsa.debian.org/med-team/community/2020-covid19-hackathon/-/wikis/NEW-Requests Thank you fo

Re: [RFS] pyrle

2020-06-20 Thread Andreas Tille
On Sat, Jun 20, 2020 at 12:36:07AM +0530, Nilesh Patra wrote: > Hi, > I've packaged pyrle - that's a new module. I've ensured that this looks > good. > The repo is here[1] > Needs review and sponsorship. Uploaded after some nitpicking changes and added to https://salsa.debian.org/med-team/comm

Re: RFS: prinseq-lite: prinseq-graphs with PCA support

2020-06-20 Thread Andreas Tille
On Fri, Jun 19, 2020 at 10:28:04PM +0200, Étienne Mollier wrote: > With the adjonction of libstatistics-pca-perl to the repository, > thanks to the Debian Perl team for its help, I finally took some > time to enable support for PCA graphs in prinseq-lite 0.20.4-5. > > The package is pushed on sals

Re: Parallel packaging attempts

2020-06-20 Thread Antoni Villalonga
Hi, While I mostly agree with Andreas and Steffen points of view, I'm starting to clash on my attempts. Mosty 'pore-c' related software... I'm trying to pick a package from spreadsheet related to 'high' priority workflows. Probably other team members are following same order. Is it possible for

[RFS] sorted-nearest

2020-06-20 Thread Nilesh Patra
Hi, I've packaged sorted-nearest - that's a new module. I've ensured that this looks good. The repo is here[1] Needs review and sponsorship. [1]: https://salsa.debian.org/med-team/sorted-nearest Thanks and regards Nilesh

Re: Parallel packaging attempts

2020-06-20 Thread Andreas Tille
Hi Antoni, On Sat, Jun 20, 2020 at 10:10:47AM +, Antoni Villalonga wrote: > While I mostly agree with Andreas and Steffen points of view, I'm starting to > clash on my attempts. Mosty 'pore-c' related software... > > I'm trying to pick a package from spreadsheet related to 'high' priority > w

Re: raxml-ng dependency not already packaged

2020-06-20 Thread Michael Crusoe
When a git submodule is being used, please check the exact commit referenced in the repository. In this case raxml-ng uses https://github.com/ddarriba/pll-modules/commit/7a0715a7d8e3c30ae86819425e876d96949d3f4d (from 2019-11-27, from the 'dev' branch, but not the latest commit from that branch) and

Re: raxml-ng dependency not already packaged

2020-06-20 Thread Andreas Tille
On Sat, Jun 20, 2020 at 03:50:28PM +0200, Michael Crusoe wrote: > When a git submodule is being used, please check the exact commit > referenced in the repository. In this case raxml-ng uses > https://github.com/ddarriba/pll-modules/commit/7a0715a7d8e3c30ae86819425e876d96949d3f4d > (from 2019-11-27

Re: pplacer - and undefined mclgUnionv reference

2020-06-20 Thread Shayan Doust
Hello, For some reason, I cannot seem to compile mcl anymore? ... Do you speak a language other than English, or a different variant of English? Consider helping us to localize HTML Tidy. For details please see https://github.com/htacg/tidy-html5/blob/master/README/LOCALIZE.md make[4]: [Makefile:

Demoting Recommends in overly large bio task

2020-06-20 Thread Andreas Tille
Hi Steffen, I've thought about our discussion in the video conference yesterday about demoting Recommends to Suggests. In principle I agree with you that task bio is to large meanwhile. I share this opinion since years and would love if we could find some better solution - possibly with some mor

Re: What is the relation ncbi-magicblast and magicblast

2020-06-20 Thread Aaron M. Ucko
Andreas Tille writes: > I did this. I'm a bit worried about those errors but if you say so > I think we can go with this. Thanks! I could in principle track down the upstream change(s) that bring this test back in sync, but I'm not sure there's much point, given that AFAICT official autobuilde

Re: pplacer - and undefined mclgUnionv reference

2020-06-20 Thread Aaron M. Ucko
Shayan Doust writes: > I have even tried adding bsdmainutils as build depends but I do not know > why "col" command cannot be found. It recently moved to a new bsdextrautils binary package, coming from the util-linux source package. Please try declaring a build dependency on bsdextrautils | bs

Re: pplacer - and undefined mclgUnionv reference

2020-06-20 Thread Andreas Tille
On Sat, Jun 20, 2020 at 09:54:10PM -0400, Aaron M. Ucko wrote: > Shayan Doust writes: > > > I have even tried adding bsdmainutils as build depends but I do not know > > why "col" command cannot be found. > > It recently moved to a new bsdextrautils binary package, coming from the > util-linux so