From mboxrd@z Thu Jan 1 00:00:00 1970 From: Ben Woodcroft Subject: Re: Update mafft to 7.245. Date: Tue, 15 Dec 2015 22:05:04 +1000 Message-ID: <567001F0.7060206@uq.edu.au> References: <5641E082.90801@uq.edu.au> <20151110151207.6c5e4693@debian-netbook> <56426E2B.10405@uq.edu.au> Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="------------020207030009080205040900" Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:54589) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1a8oM6-0007vi-OU for guix-devel@gnu.org; Tue, 15 Dec 2015 07:05:27 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1a8oM3-0003yu-Fx for guix-devel@gnu.org; Tue, 15 Dec 2015 07:05:22 -0500 Received: from mailhub2.soe.uq.edu.au ([130.102.132.209]:37906 helo=newmailhub.uq.edu.au) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1a8oM2-0003y3-Sb for guix-devel@gnu.org; Tue, 15 Dec 2015 07:05:19 -0500 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-bounces+gcggd-guix-devel=m.gmane.org@gnu.org To: Ricardo Wurmus Cc: "guix-devel@gnu.org" This is a multi-part message in MIME format. --------------020207030009080205040900 Content-Type: text/plain; charset=utf-8; format=flowed Content-Transfer-Encoding: quoted-printable X-MIME-Autoconverted: from 8bit to quoted-printable by newmailhub.uq.edu.au id tBFC57Tq029392 On 11/12/15 02:16, Ricardo Wurmus wrote: > Ben Woodcroft writes: > >> 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-inpu= ts? >>> 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 ar= e >> 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 wh= en >> the shell script is difficult to exhaustively test. WDYT? > I looked at the instances of =E2=80=9Cperl=E2=80=9D, =E2=80=9Cawk=E2=80= =9D, and =E2=80=9Cgrep=E2=80=9D and they seem > manageable. I didn=E2=80=99t test this but attached is a different ver= sion of > your patch that does what I suggested. It might work. Could you try t= o > confirm that it=E2=80=99s okay? > > What do you think? I think you are quite valiant. As I say, I cannot be confident in my=20 testing (even those in the readme). The diff looked mostly fine by eye,=20 but there was some issues near the end which mangled things somewhat=20 (although maybe not the result, not sure). How's the attached? I upped=20 version too. OK? Thanks, ben --------------020207030009080205040900 Content-Type: text/x-patch; name="0001-PATCH-gnu-mafft-Update-to-7.267.patch" Content-Disposition: attachment; filename="0001-PATCH-gnu-mafft-Update-to-7.267.patch" Content-Transfer-Encoding: 7bit >From e256089eadca19e31fa986d2ce7c13f7fbc3311b Mon Sep 17 00:00:00 2001 From: Ben Woodcroft Date: Tue, 15 Dec 2015 20:34:52 +1000 Subject: [PATCH] [PATCH] gnu: mafft: Update to 7.267. * gnu/packages/bioinformatics.scm (mafft): Update to 7.267. [arguments]: Don't include mafft-homologs manpage. [inputs]: Add gawk and grep. [propagated-inputs]: Add coreutils. --- gnu/packages/bioinformatics.scm | 23 ++++++++++++++++++++--- 1 file changed, 20 insertions(+), 3 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 7c573e1..21b85db 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) @@ -1690,7 +1691,7 @@ sequencing tag position and orientation.") (define-public mafft (package (name "mafft") - (version "7.221") + (version "7.267") (source (origin (method url-fetch) (uri (string-append @@ -1699,7 +1700,7 @@ sequencing tag position and orientation.") (file-name (string-append name "-" version ".tgz")) (sha256 (base32 - "0xi7klbsgi049vsrk6jiwh9wfj3b770gz3c8c7zwij448v0dr73d")))) + "1xl6xq1rfxkws0svrlhyqxhhwbv6r77jwblsdpcyiwzsscw6wlk0")))) (build-system gnu-build-system) (arguments `(#:tests? #f ; no automated tests, though there are tests in the read me @@ -1720,6 +1721,9 @@ 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") @@ -1732,9 +1736,22 @@ sequencing tag position and orientation.") (("^\t\\$\\(INSTALL\\) -m 644 \\$\\(MANPAGES\\) \ \\$\\(DESTDIR\\)\\$\\(LIBDIR\\)") "#")) #t)) + (add-after 'enter-dir 'patch-paths + (lambda* (#:key inputs #:allow-other-keys) + (substitute* '("pairash.c" + "mafft.tmpl") + (("perl") (which "perl")) + (("([\"`| ])awk" _ prefix) + (string-append prefix (which "awk"))) + (("grep") (which "grep"))) + #t)) (delete 'configure)))) (inputs - `(("perl" ,perl))) + `(("perl" ,perl) + ("gawk" ,gawk) + ("grep" ,grep))) + (propagated-inputs + `(("coreutils" ,coreutils))) (home-page "http://mafft.cbrc.jp/alignment/software/") (synopsis "Multiple sequence alignment program") (description -- 2.5.0 --------------020207030009080205040900--