From mboxrd@z Thu Jan 1 00:00:00 1970 From: ludo@gnu.org (Ludovic =?utf-8?Q?Court=C3=A8s?=) Subject: Re: [PATCH] Add (minimal) BioPerl. Date: Sat, 06 Jun 2015 20:05:37 +0200 Message-ID: <8738244sr2.fsf@gnu.org> References: <87sia44tjs.fsf@gnu.org> <87d218wwp9.fsf@mdc-berlin.de> 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]:37497) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1Z1ITY-0004nu-F3 for guix-devel@gnu.org; Sat, 06 Jun 2015 14:05:45 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1Z1ITV-0001oL-5a for guix-devel@gnu.org; Sat, 06 Jun 2015 14:05:44 -0400 Received: from fencepost.gnu.org ([2001:4830:134:3::e]:51371) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1Z1ITV-0001oF-1Y for guix-devel@gnu.org; Sat, 06 Jun 2015 14:05:41 -0400 In-Reply-To: <87d218wwp9.fsf@mdc-berlin.de> (Ricardo Wurmus's message of "Sat, 6 Jun 2015 19:52:50 +0200") 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-bounces+gcggd-guix-devel=m.gmane.org@gnu.org To: Ricardo Wurmus Cc: guix-devel Ricardo Wurmus skribis: > Ludovic Court=C3=A8s writes: > >> Ricardo Wurmus skribis: >> >>> From e8cffdb9e7a2447657b3f700b2f0beb00ad0f98e Mon Sep 17 00:00:00 2001 >>> From: Ricardo Wurmus >>> Date: Wed, 3 Jun 2015 17:44:20 +0200 >>> Subject: [PATCH] gnu: Add BioPerl. >>> >>> * gnu/packages/bioinformatics.scm (bioperl-minimal): New variable. >> >> [...] >> >>> +(define-public bioperl-minimal >>> + (package >>> + (name "bioperl-minimal") >> >> So is it meant to be used as a Perl library, as a standalone executable, >> or both? > > It's a library and a collection of perl executables using the library, > so I suppose "bioperl-minimal" would be appropriate? Yeah that=E2=80=99s fine with me. >>> + (native-search-paths (list (search-path-specification >>> + (variable "PERL5LIB") >>> + (files '("lib/perl5/site_perl"))))) >> >> Why is it needed? At first sight it looks wrong because PERL5LIB is >> =E2=80=9Cowned=E2=80=9D by Perl itself. >> >> If there=E2=80=99s an executable that needs to find the libs listed in >> =E2=80=98propagated-inputs=E2=80=99, the best way would be to use =E2=80= =98wrap-program=E2=80=99, I >> think. > > That's for the executables to find the library contained in this package > as well as the propagated Perl libraries. There are *many* executables, > which made me shy away from wrapping each of them to be run with the > PERL5LIB variable set. There are two cases: 1. When using BioPerl as a library, users will also have Perl installed, so =E2=80=98guix package=E2=80=99 will report the right val= ue for PERL5LIB. No problem here. 2. When using just the executables, Perl might be missing from the profile. =E2=80=98wrap-program=E2=80=99 looks best to me for that, ev= en if there are many executables. WDYT? Thanks, Ludo=E2=80=99.