gnu: Add mafft.

* gnu/packages/bioinformatics.scm (mafft): New variable.
This commit is contained in:
Ben Woodcroft 2015-09-12 22:10:20 +10:00 committed by Ricardo Wurmus
parent e864722731
commit 41ddebdd2a

View file

@ -1545,6 +1545,64 @@ (define-public macs
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
(("splittbfast disttbfast tbfast mafft-profile 2cl 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
(("^\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
"http://mafft.cbrc.jp/alignment/software/license.txt"
"BSD-3 with different formatting"))))
(define-public metabat
(package