From mboxrd@z Thu Jan 1 00:00:00 1970 From: Ricardo Wurmus Subject: Re: Update mafft to 7.245. Date: Thu, 10 Dec 2015 17:16:09 +0100 Message-ID: References: <5641E082.90801@uq.edu.au> <20151110151207.6c5e4693@debian-netbook> <56426E2B.10405@uq.edu.au> Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="=-=-=" Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:37687) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1a73tM-0002vG-NH for guix-devel@gnu.org; Thu, 10 Dec 2015 11:16:34 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1a73tG-0003IW-MO for guix-devel@gnu.org; Thu, 10 Dec 2015 11:16:28 -0500 Received: from sinope.bbbm.mdc-berlin.de ([141.80.25.23]:53090) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1a73tG-0003I1-8D for guix-devel@gnu.org; Thu, 10 Dec 2015 11:16:22 -0500 In-Reply-To: <56426E2B.10405@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-bounces+gcggd-guix-devel=m.gmane.org@gnu.org To: Ben Woodcroft Cc: "guix-devel@gnu.org" --=-=-= Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: quoted-printable 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-input= s? >> Often that's enough to take care of it. > The main program 'mafft' is actually a reasonably long shell script,=20 > which itself calls awk, grep, perl, etc. collectively many times (>100 = I=20 > would guess). I think it is intended to be run where these programs are= =20 > available. I could do as Ricardo suggests and run substitute* but this=20 > seems a bit error-prone and not very future-proof to me, especially whe= n=20 > 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 versi= on of your patch that does what I suggested. It might work. Could you try to confirm that it=E2=80=99s okay? What do you think? --=-=-= Content-Type: text/x-patch Content-Disposition: inline; filename="0001-gnu-mafft-Update-to-7.245.patch" >From 7f52cd8576df7cb4355d3281ca0d00fc661a0221 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]: 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 64dd280..0a3de06 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) @@ -1789,7 +1790,7 @@ 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 @@ -1798,7 +1799,7 @@ 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 @@ -1819,6 +1820,9 @@ 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") @@ -1831,9 +1835,22 @@ 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 -- 2.1.0 --=-=-= Content-Type: text/plain ~~ Ricardo --=-=-=--