From mboxrd@z Thu Jan 1 00:00:00 1970 From: Ben Woodcroft Subject: Re: [PATCH] gnu: Add seqtk. Date: Sat, 10 Sep 2016 14:03:36 +1000 Message-ID: <73fee0ea-8e2b-2ef6-1f55-e43be40feb5c@uq.edu.au> References: <20150718090748.GA26418@jocasta.intra> <20160909110834.8581-1-donttrustben@gmail.com> <871t0ts0yu.fsf@ike.i-did-not-set--mail-host-address--so-tickle-me> Mime-Version: 1.0 Content-Type: text/plain; charset=windows-1252; format=flowed Content-Transfer-Encoding: 7bit Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:60518) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1biZWI-0006j3-HZ for guix-devel@gnu.org; Sat, 10 Sep 2016 00:03:59 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1biZWD-00010s-G4 for guix-devel@gnu.org; Sat, 10 Sep 2016 00:03:57 -0400 Received: from mailhub2.soe.uq.edu.au ([130.102.132.209]:55298 helo=newmailhub.uq.edu.au) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1biZWC-00010V-Ti for guix-devel@gnu.org; Sat, 10 Sep 2016 00:03:53 -0400 In-Reply-To: <871t0ts0yu.fsf@ike.i-did-not-set--mail-host-address--so-tickle-me> List-Id: "Development of GNU Guix and the GNU System distribution." List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-devel-bounces+gcggd-guix-devel=m.gmane.org@gnu.org Sender: "Guix-devel" To: Marius Bakke , Ben Woodcroft , guix-devel@gnu.org On 09/09/16 22:37, Marius Bakke wrote: > Ben Woodcroft writes: > >> Well, despite the lightness of my touch, it seems the licensing is in now in >> order. I've updated the package, here's an updated patch. Better? > I don't think this was intended to be a commit message? :) No indeed, I was responding to a thread so old I suspect it was before your time. > The program seems to bundle {khash,kseq}.h from htslib. Could you try > replacing them with the files directly from htslib? There are quite a > few examples of doing this already in bioinformatics.scm. I see your point, though I'm not sure that htslib is really the home of those files, and anyway our htslib doesn't provide them as an output since they are not a shared library (I believe). I've always been a bit fuzzy on what the official policy is, to what extent we should remove bundled code, so I'm happy to be corrected. In this case since there is clear precedent I don't think we should bother removing the bundled files. > I also think the original description from github is better: > "Toolkit for processing sequences in FASTA/Q formats". How about "Toolkit for processing biological sequences in FASTA/Q format"? I wanted to make it understandable in a more general context. I'll push in the next day or two unless there are further comments. Thanks for the review. ben