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gnu: mafft: Update to 7.267.

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* gnu/packages/bioinformatics.scm (mafft): Update to 7.267.
[arguments]: Don't include mafft-homologs manpage.
[inputs]: Add gawk and grep.
[propagated-inputs]: Add coreutils.
This commit is contained in:
Ben Woodcroft 2015-12-15 20:34:52 +10:00 • committed by Ricardo Wurmus
parent 1ef3f91a70
commit 02f35bb5a7
1 changed files with 20 additions and 3 deletions
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23
gnu/packages/bioinformatics.scm
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@ -40,6 +40,7 @@
#:use-module (gnu packages compression) #:use-module (gnu packages compression)
#:use-module (gnu packages cpio) #:use-module (gnu packages cpio)
#:use-module (gnu packages file) #:use-module (gnu packages file)
#:use-module (gnu packages gawk)
#:use-module (gnu packages java) #:use-module (gnu packages java)
#:use-module (gnu packages linux) #:use-module (gnu packages linux)
#:use-module (gnu packages machine-learning) #:use-module (gnu packages machine-learning)
@ -1690,7 +1691,7 @@ sequencing tag position and orientation.")
(define-public mafft (define-public mafft
(package (package
(name "mafft") (name "mafft")
(version "7.221") (version "7.267")
(source (origin (source (origin
(method url-fetch) (method url-fetch)
(uri (string-append (uri (string-append
@ -1699,7 +1700,7 @@ sequencing tag position and orientation.")
(file-name (string-append name "-" version ".tgz")) (file-name (string-append name "-" version ".tgz"))
(sha256 (sha256
(base32 (base32
"0xi7klbsgi049vsrk6jiwh9wfj3b770gz3c8c7zwij448v0dr73d")))) "1xl6xq1rfxkws0svrlhyqxhhwbv6r77jwblsdpcyiwzsscw6wlk0"))))
(build-system gnu-build-system) (build-system gnu-build-system)
(arguments (arguments
`(#:tests? #f ; no automated tests, though there are tests in the read me `(#:tests? #f ; no automated tests, though there are tests in the read me
@ -1720,6 +1721,9 @@ sequencing tag position and orientation.")
;; remove mafft-homologs.rb from SCRIPTS ;; remove mafft-homologs.rb from SCRIPTS
(("^SCRIPTS = mafft mafft-homologs.rb") (("^SCRIPTS = mafft mafft-homologs.rb")
"SCRIPTS = mafft") "SCRIPTS = mafft")
;; remove mafft-homologs from MANPAGES
(("^MANPAGES = mafft.1 mafft-homologs.1")
"MANPAGES = mafft.1")
;; remove mafft-distance from PROGS ;; remove mafft-distance from PROGS
(("^PROGS = dvtditr dndfast7 dndblast sextet5 mafft-distance") (("^PROGS = dvtditr dndfast7 dndblast sextet5 mafft-distance")
"PROGS = dvtditr dndfast7 dndblast sextet5") "PROGS = dvtditr dndfast7 dndblast sextet5")
@ -1732,9 +1736,22 @@ sequencing tag position and orientation.")
(("^\t\\$\\(INSTALL\\) -m 644 \\$\\(MANPAGES\\) \ (("^\t\\$\\(INSTALL\\) -m 644 \\$\\(MANPAGES\\) \
\\$\\(DESTDIR\\)\\$\\(LIBDIR\\)") "#")) \\$\\(DESTDIR\\)\\$\\(LIBDIR\\)") "#"))
#t)) #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)))) (delete 'configure))))
(inputs (inputs
`(("perl" ,perl))) `(("perl" ,perl)
("gawk" ,gawk)
("grep" ,grep)))
(propagated-inputs
`(("coreutils" ,coreutils)))
(home-page "http://mafft.cbrc.jp/alignment/software/") (home-page "http://mafft.cbrc.jp/alignment/software/")
(synopsis "Multiple sequence alignment program") (synopsis "Multiple sequence alignment program")
(description (description