From mboxrd@z Thu Jan 1 00:00:00 1970 From: Ricardo Wurmus Subject: Re: [PATCH] Add Ribotaper. Date: Thu, 7 Jul 2016 15:45:05 +0200 Message-ID: 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" Content-Transfer-Encoding: quoted-printable Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:35619) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1bL9cE-0008Gk-U8 for guix-devel@gnu.org; Thu, 07 Jul 2016 09:45:20 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1bL9cA-00010c-NH for guix-devel@gnu.org; Thu, 07 Jul 2016 09:45:17 -0400 Received: from venus.bbbm.mdc-berlin.de ([141.80.25.30]:56266) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1bL9cA-00010G-DM for guix-devel@gnu.org; Thu, 07 Jul 2016 09:45:14 -0400 In-Reply-To: <577E59D2.3010107@uq.edu.au> 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: Ben Woodcroft Cc: guix-devel@gnu.org 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 bedto= ols >> 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 "ribotap= er" but >> also "bedtools-for-ribotaper". >> >> Do you think I should rather name it "bedtools-2.18" and make it publi= c so >> that users can install it? > > This would be my preference, IIUC this is the current way we do this. I= s=20 > there any difference from previous times we've had to include outdated=20 > packages? I actually prefer to just offer =E2=80=9Cbedtools-2.18=E2=80=9D without r= estricting it to just ribotaper, but we=E2=80=99d have to ensure that this version stay= s 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 packag= es 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 this= 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. > Note that I just updated bedtools, although I imagine that won't help h= ere. No, the format hasn=E2=80=99t changed back. Ribotaper was not developed = with the more recent versions, which all output more columns. ~~ Ricardo