From mboxrd@z Thu Jan 1 00:00:00 1970 From: Ricardo Wurmus Subject: Re: [PATCH] Add (minimal) BioPerl. Date: Sat, 6 Jun 2015 19:52:50 +0200 Message-ID: <87d218wwp9.fsf@mdc-berlin.de> References: <87sia44tjs.fsf@gnu.org> 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]:36391) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1Z1IHI-0003bu-BV for guix-devel@gnu.org; Sat, 06 Jun 2015 13:53:05 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1Z1IHD-000732-Bp for guix-devel@gnu.org; Sat, 06 Jun 2015 13:53:04 -0400 In-Reply-To: <87sia44tjs.fsf@gnu.org> 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: Ludovic =?utf-8?Q?Court=C3=A8s?= Cc: guix-devel 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? >> + (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. ~~ Ricardo