Note that the "extensions" listed on the website are research/non-profit
only, and so not fit for inclusion.
>From b966b0c8ab9b194bbb7089cc4b4e3a9727862691 Mon Sep 17 00:00:00 2001
From: Ben Woodcroft <donttrust...@gmail.com>
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/bioinformatics.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)))
+(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 readme
+ #:make-flags (list (string-append "PREFIX=" (assoc-ref %outputs "out"))
+ (string-append "BINDIR=" (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-profile,
+ ;; mafft-distance mafft-homologs.rb
+ (add-after 'enter-dir 'patch-makefile
+ (lambda _
+ (substitute* "Makefile"
+ (("^SCRIPTS = mafft mafft-homologs.rb")
+ "SCRIPTS = mafft")
+ (((string-append "^PROGS = dvtditr dndfast7 dndblast"
+ " sextet5 mafft-distance"))
+ "PROGS = dvtditr dndfast7 dndblast sextet5")
+ (((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 for unix-like operating systems")
+ (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 <â¼200 sequences) and FFT-NS-2 (fast; for alignment of <â¼30,000
+sequences).")
+ (license (license:non-copyleft "file://license"
+ "See license in the distribution."))))
(define-public metabat
(package
--
2.4.3
