From mboxrd@z Thu Jan 1 00:00:00 1970 From: Ben Woodcroft Subject: [PATCH] Add MAFFT. Date: Thu, 23 Jul 2015 22:43:31 +1000 Message-ID: <55B0E173.1030406@uq.edu.au> Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="------------050000050602030106060300" Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:38578) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1ZIFqm-000263-Bd for guix-devel@gnu.org; Thu, 23 Jul 2015 08:43:49 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1ZIFqh-0000I7-Aq for guix-devel@gnu.org; Thu, 23 Jul 2015 08:43:48 -0400 Received: from mailhub1.soe.uq.edu.au ([130.102.132.208]:36201 helo=newmailhub.uq.edu.au) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1ZIFqg-0000HU-Oj for guix-devel@gnu.org; Thu, 23 Jul 2015 08:43:43 -0400 Received: from smtp2.soe.uq.edu.au (smtp2.soe.uq.edu.au [10.138.113.41]) by newmailhub.uq.edu.au (8.14.5/8.14.5) with ESMTP id t6NChZ7k037870 for ; Thu, 23 Jul 2015 22:43:35 +1000 Received: from [192.168.1.101] ([103.25.181.216]) (authenticated bits=0) by smtp2.soe.uq.edu.au (8.14.5/8.14.5) with ESMTP id t6NChWQW041210 (version=TLSv1/SSLv3 cipher=DHE-RSA-AES128-SHA bits=128 verify=NOT) for ; Thu, 23 Jul 2015 22:43:34 +1000 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: "guix-devel@gnu.org" This is a multi-part message in MIME format. --------------050000050602030106060300 Content-Type: text/plain; charset=utf-8; format=flowed Content-Transfer-Encoding: 7bit Note that the "extensions" listed on the website are research/non-profit only, and so not fit for inclusion. --------------050000050602030106060300 Content-Type: text/x-patch; name="0001-gnu-Add-mafft.patch" Content-Disposition: attachment; filename="0001-gnu-Add-mafft.patch" Content-Transfer-Encoding: quoted-printable X-MIME-Autoconverted: from 8bit to quoted-printable by newmailhub.uq.edu.au id t6NChZ7k037870 >From b966b0c8ab9b194bbb7089cc4b4e3a9727862691 Mon Sep 17 00:00:00 2001 From: Ben Woodcroft Date: Thu, 23 Jul 2015 22:42:17 +1000 Subject: [PATCH] gnu: Add mafft. * gnu/packages/bioinformatics.scm (mafft): New variable --- gnu/packages/bioinformatics.scm | 57 +++++++++++++++++++++++++++++++++++= ++++++ 1 file changed, 57 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatic= s.scm index 78cd3ce..a09b89e 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1394,6 +1394,63 @@ resolution of binding sites through combining the = information of both sequencing tag position and orientation.") (license license:bsd-3))) =20 +(define-public mafft + (package + (name "mafft") + (version "7.221") + (source (origin + (method url-fetch) + (uri (string-append + "http://mafft.cbrc.jp/alignment/software/mafft-" ver= sion + "-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 r= eadme + #:make-flags (list (string-append "PREFIX=3D" (assoc-ref %outputs= "out")) + (string-append "BINDIR=3D" (string-append + (assoc-ref %outputs = "out") + "/bin"))) + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'enter-dir + (lambda _ (chdir "core") #t)) + ;; on advice from the MAFFT authors, do not distribute mafft-pr= ofile, + ;; mafft-distance mafft-homologs.rb + (add-after 'enter-dir 'patch-makefile + (lambda _ + (substitute* "Makefile" + (("^SCRIPTS =3D mafft mafft-homologs.rb") + "SCRIPTS =3D mafft") + (((string-append "^PROGS =3D dvtditr dndfast7 dn= dblast" + " sextet5 mafft-distance")) + "PROGS =3D dvtditr dndfast7 dndblast sextet5") + (((string-append "splittbfast disttbfast tbfast = " + "mafft-profile f2cl mccaskillwr= ap")) + "splittbfast disttbfast tbfast f2cl mccaskillwr= ap") + (("^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 for unix-like operating system= s") + (description + "MAFFT offers a range of multiple alignment methods for nucleotide = and +protein sequences. For instance, it offers L-INS-i (accurate; for align= ment +of <=E2=88=BC200 sequences) and FFT-NS-2 (fast; for alignment of <=E2=88= =BC30,000 +sequences).") + (license (license:non-copyleft "file://license" + "See license in the distribution.")))) =20 (define-public metabat (package --=20 2.4.3 --------------050000050602030106060300--