From mboxrd@z Thu Jan 1 00:00:00 1970 From: Ben Woodcroft Subject: Re: Update mafft to 7.245. Date: Wed, 11 Nov 2015 08:22:35 +1000 Message-ID: <56426E2B.10405@uq.edu.au> References: <5641E082.90801@uq.edu.au> <20151110151207.6c5e4693@debian-netbook> Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="------------070705070509030803060602" Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:57736) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1ZwHJS-0006kM-BC for guix-devel@gnu.org; Tue, 10 Nov 2015 17:22:51 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1ZwHJP-0004Sd-6c for guix-devel@gnu.org; Tue, 10 Nov 2015 17:22:50 -0500 Received: from mailhub2.soe.uq.edu.au ([130.102.132.209]:45116 helo=newmailhub.uq.edu.au) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1ZwHJO-0004SN-KJ for guix-devel@gnu.org; Tue, 10 Nov 2015 17:22:47 -0500 In-Reply-To: <20151110151207.6c5e4693@debian-netbook> 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: Efraim Flashner Cc: "guix-devel@gnu.org" This is a multi-part message in MIME format. --------------070705070509030803060602 Content-Type: text/plain; charset=utf-8; format=flowed Content-Transfer-Encoding: 7bit Two reviews in record time, nice. On 10/11/15 23:12, Efraim Flashner wrote: > On Tue, 10 Nov 2015 22:18:10 +1000 > Ben Woodcroft wrote: > >> Also had to fix the inputs. Hard not to notice these things in the >> environment container - worked well thanks. > Do they need to be propagated inputs? Did you try them as native-inputs? > Often that's enough to take care of it. The main program 'mafft' is actually a reasonably long shell script, which itself calls awk, grep, perl, etc. collectively many times (>100 I would guess). I think it is intended to be run where these programs are available. I could do as Ricardo suggests and run substitute* but this seems a bit error-prone and not very future-proof to me, especially when the shell script is difficult to exhaustively test. WDYT? Note that mafft is probably not going to remain as a leaf because a number of bioinformatic tools not yet packaged rely on it. > Also, instead of: > Fix inputs. > the commit message is more along the lines of: > [inputs]: Move inputs to propagated-inputs and add missing dependencies. > but I normally have to check against older commit messages to see what others > are doing and I try to copy that. Hopefully the attached is a better attempt? I also added another small improvement, not distributing the manpage of a program that is excluded from distribution. Thanks. --------------070705070509030803060602 Content-Type: text/x-patch; name="0001-gnu-mafft-Update-to-7.245.patch" Content-Transfer-Encoding: 7bit Content-Disposition: attachment; filename="0001-gnu-mafft-Update-to-7.245.patch" >From e05c50d2b40bf3290ec247223b3504429e9ad44e Mon Sep 17 00:00:00 2001 From: Ben Woodcroft Date: Wed, 11 Nov 2015 08:04:55 +1000 Subject: [PATCH] gnu: mafft: Update to 7.245. * gnu/packages/bioinformatics.scm (mafft): Update to 7.245. [arguments]: Don't include mafft-homologs manpage. [inputs]: Move inputs to propagated-inputs and add missing dependencies. --- gnu/packages/bioinformatics.scm | 15 +++++++++++---- 1 file changed, 11 insertions(+), 4 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index f13e405..9ee669e 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -40,6 +40,7 @@ #:use-module (gnu packages compression) #:use-module (gnu packages cpio) #:use-module (gnu packages file) + #:use-module (gnu packages gawk) #:use-module (gnu packages java) #:use-module (gnu packages linux) #:use-module (gnu packages machine-learning) @@ -1688,7 +1689,7 @@ sequencing tag position and orientation.") (define-public mafft (package (name "mafft") - (version "7.221") + (version "7.245") (source (origin (method url-fetch) (uri (string-append @@ -1697,7 +1698,7 @@ sequencing tag position and orientation.") (file-name (string-append name "-" version ".tgz")) (sha256 (base32 - "0xi7klbsgi049vsrk6jiwh9wfj3b770gz3c8c7zwij448v0dr73d")))) + "0m1l7gdrmfxjw54d3a0g18w6rwqrra9w9zvxix7dcddw6d1qyir2")))) (build-system gnu-build-system) (arguments `(#:tests? #f ; no automated tests, though there are tests in the read me @@ -1718,6 +1719,9 @@ sequencing tag position and orientation.") ;; remove mafft-homologs.rb from SCRIPTS (("^SCRIPTS = mafft mafft-homologs.rb") "SCRIPTS = mafft") + ;; remove mafft-homologs from MANPAGES + (("^MANPAGES = mafft.1 mafft-homologs.1") + "MANPAGES = mafft.1") ;; remove mafft-distance from PROGS (("^PROGS = dvtditr dndfast7 dndblast sextet5 mafft-distance") "PROGS = dvtditr dndfast7 dndblast sextet5") @@ -1731,8 +1735,11 @@ sequencing tag position and orientation.") \\$\\(DESTDIR\\)\\$\\(LIBDIR\\)") "#")) #t)) (delete 'configure)))) - (inputs - `(("perl" ,perl))) + (propagated-inputs + `(("perl" ,perl) + ("gawk" ,gawk) + ("coreutils" ,coreutils) + ("grep" ,grep))) (home-page "http://mafft.cbrc.jp/alignment/software/") (synopsis "Multiple sequence alignment program") (description -- 2.4.3 --------------070705070509030803060602--