From mboxrd@z Thu Jan 1 00:00:00 1970 From: Ben Woodcroft Subject: Re: [PATCH] Add MAFFT. Date: Sat, 12 Sep 2015 22:20:11 +1000 Message-ID: <55F4187B.8020804@uq.edu.au> References: <55B0E173.1030406@uq.edu.au> <876158xcoo.fsf@mdc-berlin.de> <55B44F96.8050808@uq.edu.au> <20150726094338.GA24898@debian> <20150726102915.GA32496@debian> <55BBF9E6.50403@uq.edu.au> <87d1ybhypp.fsf@gnu.org> <20150907085519.GA4513@debian> Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="------------090603090907010605080107" Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:44037) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1ZajnH-0006ny-Am for guix-devel@gnu.org; Sat, 12 Sep 2015 08:20:36 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1ZajnC-00043l-St for guix-devel@gnu.org; Sat, 12 Sep 2015 08:20:35 -0400 Received: from mailhub1.soe.uq.edu.au ([130.102.132.208]:41151 helo=newmailhub.uq.edu.au) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1ZajnC-0003vU-7F for guix-devel@gnu.org; Sat, 12 Sep 2015 08:20:30 -0400 In-Reply-To: <20150907085519.GA4513@debian> 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: Andreas Enge , Ricardo Wurmus Cc: "guix-devel@gnu.org" This is a multi-part message in MIME format. --------------090603090907010605080107 Content-Type: text/plain; charset=iso-8859-15; format=flowed Content-Transfer-Encoding: quoted-printable X-MIME-Autoconverted: from 8bit to quoted-printable by newmailhub.uq.edu.au id t8CCKE3Y034397 On 07/09/15 18:55, Andreas Enge wrote: > On Tue, Aug 25, 2015 at 10:58:42PM +0200, Ludovic Court=E8s wrote: >> It seems this message was left unanswered. Andreas? > I had a cursory look at the patch, here are some comments: > > [..] >> +protein sequences. For instance, it offers L-INS-i (accurate; for al= ignment >> +of Is this an artefact of the mailer? > > I did not check whether the package passes "guix lint". > > Could you send an updated patch? Attached - I was only able to remove some of the long string-append=20 lines. Apologies for that second "patch" - not intentional. Thanks for=20 the review. I've changed the character to a different "~" so hopefully=20 more standard now. Guix lint doesn't complain. ben --------------090603090907010605080107 Content-Type: text/x-patch; name="0001-gnu-Add-mafft.patch" Content-Disposition: attachment; filename="0001-gnu-Add-mafft.patch" Content-Transfer-Encoding: 7bit >From 0796e8be05977e6d30eab787a1550bd8d1f12b2d Mon Sep 17 00:00:00 2001 From: Ben Woodcroft Date: Sat, 12 Sep 2015 22:10:20 +1000 Subject: [PATCH] gnu: Add mafft. * gnu/packages/bioinformatics.scm (mafft): New variable. --- gnu/packages/bioinformatics.scm | 60 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 60 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 03eb2df..e0b7e40 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1543,6 +1543,66 @@ resolution of binding sites through combining the information of both sequencing tag position and orientation.") (license license:bsd-3))) +(define-public mafft + (package + (name "mafft") + (version "7.221") + (source (origin + (method url-fetch) + (uri (string-append + "http://mafft.cbrc.jp/alignment/software/mafft-" version + "-without-extensions-src.tgz")) + (file-name (string-append name "-" version ".tgz")) + (sha256 + (base32 + "0xi7klbsgi049vsrk6jiwh9wfj3b770gz3c8c7zwij448v0dr73d")))) + (build-system gnu-build-system) + (arguments + `(#:tests? #f ; no automated tests, though there are tests in the read me + #:make-flags (let ((out (assoc-ref %outputs "out"))) + (list (string-append "PREFIX=" out) + (string-append "BINDIR=" + (string-append out "/bin")))) + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'enter-dir + (lambda _ (chdir "core") #t)) + (add-after 'enter-dir 'patch-makefile + (lambda _ + ;; on advice from the MAFFT authors, there is no need to + ;; distribute mafft-profile, mafft-distance, or + ;; mafft-homologs.rb as they are too "specialised". + (substitute* "Makefile" + ;; remove mafft-homologs.rb from SCRIPTS + (("^SCRIPTS = mafft mafft-homologs.rb") + "SCRIPTS = mafft") + ;; remove mafft-distance from PROGS + (("^PROGS = dvtditr dndfast7 dndblast sextet5 mafft-distance") + "PROGS = dvtditr dndfast7 dndblast sextet5") + ;; remove mafft-profile from PROGS + (((string-append "splittbfast disttbfast tbfast mafft-profile" + " f2cl mccaskillwrap")) + "splittbfast disttbfast tbfast f2cl mccaskillwrap") + (("^rm -f mafft-profile mafft-profile.exe") "#") + (("^rm -f mafft-distance mafft-distance.exe") ")#") + ;; do not install MAN pages in libexec folder + (((string-append "^\t\\$\\(INSTALL\\) -m 644 \\$\\(MANPAGES" + "\\) \\$\\(DESTDIR\\)\\$\\(LIBDIR\\)")) + "#")) + #t)) + (delete 'configure)))) + (inputs + `(("perl" ,perl))) + (home-page "http://mafft.cbrc.jp/alignment/software/") + (synopsis + "Multiple sequence alignment program") + (description + "MAFFT offers a range of multiple alignment methods for nucleotide and +protein sequences. For instance, it offers L-INS-i (accurate; for alignment +of <~200 sequences) and FFT-NS-2 (fast; for alignment of <~30,000 +sequences).") + (license (license:non-copyleft "file://license" + "See license in the distribution.")))) (define-public metabat (package -- 2.4.3 --------------090603090907010605080107--