From mboxrd@z Thu Jan 1 00:00:00 1970 From: Ben Woodcroft Subject: Re: [PATCH] Add Ribotaper. Date: Sat, 9 Jul 2016 08:52:05 +1000 Message-ID: <57802E95.1020305@uq.edu.au> References: <20160707092629.23884-1-ricardo.wurmus@mdc-berlin.de> <577E59D2.3010107@uq.edu.au> Mime-Version: 1.0 Content-Type: text/plain; charset=utf-8; format=flowed Content-Transfer-Encoding: quoted-printable Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:52113) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1bLed9-0006fT-Lw for guix-devel@gnu.org; Fri, 08 Jul 2016 18:52:20 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1bLed3-00012d-Kq for guix-devel@gnu.org; Fri, 08 Jul 2016 18:52:18 -0400 Received: from mailhub2.soe.uq.edu.au ([130.102.132.209]:37992 helo=newmailhub.uq.edu.au) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1bLed3-00012Q-0p for guix-devel@gnu.org; Fri, 08 Jul 2016 18:52:13 -0400 In-Reply-To: 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: Ricardo Wurmus Cc: guix-devel@gnu.org On 07/07/16 23:45, Ricardo Wurmus wrote: > Ben Woodcroft writes: > >> On 07/07/16 19:26, Ricardo Wurmus wrote: >>> Hi Guix, >>> >>> this patch adds a bioinformatics tool called "Ribotaper". It needs a= somewhat >>> older version of bedtools, because the output format produced by bedt= ools >>> changed after version 2.18.0 (they don't seem to care about semantic >>> versioning). This is why this patch not only adds a variable "ribota= per" but >>> also "bedtools-for-ribotaper". >>> >>> Do you think I should rather name it "bedtools-2.18" and make it publ= ic so >>> that users can install it? >> This would be my preference, IIUC this is the current way we do this. = Is >> there any difference from previous times we've had to include outdated >> packages? > I actually prefer to just offer =E2=80=9Cbedtools-2.18=E2=80=9D without= restricting it > to just ribotaper, but we=E2=80=99d have to ensure that this version st= ays > around (adding a comment on top should be enough). > > We currently have =E2=80=9Cguile-for-guile-emacs=E2=80=9D, which offers= a variant of > Guile, but the situation is slightly different here. We also have > =E2=80=9Carmadillo-for-rcpparmadillo=E2=80=9D. In both cases, the pack= ages are not > private. In the former case the package name differs, but in the case > of armadillo it=E2=80=99s only the variable name that indicates that th= is is > special. > > I think in the ribotaper/bedtools case we should just name the variable > =E2=80=9Cbedtools-2.18=E2=80=9D and make it public. I agree with should call it 'bedtools-2.18' and make it public (but with=20 a comment explaining why the old version is kept), just as in e.g.=20 'python-flake8-2.2.4'. Are you suggesting we keep bedtools-2.18 even if ribotaper updates to a=20 newer version? I thought accepted practice was to delete old packages=20 when they are no longer needed. The patch LGTM otherwise, except that I would unpack 'ORF' and use the=20 term 'ribo-seq' in the description. I've never looking at ribo-seq data=20 before and I'm not familiar, so I wasn't sure what 'ribosome profiling'=20 meant exactly e.g. is it measuring the amount of ribosome in a cell? I=20 realise that isn't true, just illustrating the point. Perhaps I am too=20 naive. ben