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authorBen Woodcroft <donttrustben@gmail.com>2015-12-15 20:34:52 +1000
committerRicardo Wurmus <ricardo.wurmus@mdc-berlin.de>2015-12-21 15:16:01 +0100
commit02f35bb5a755984c9c419101d53f59f6274a0b8a (patch)
tree78fcec156c6b335f106d2e46db37d92688052f85 /gnu/packages/bioinformatics.scm
parent1ef3f91a702e19b01aff2e85b7ea2abe1f7579a1 (diff)
gnu: mafft: Update to 7.267.
* 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.
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
-rw-r--r--gnu/packages/bioinformatics.scm23
1 files changed, 20 insertions, 3 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 7c573e1626..21b85db903 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -40,6 +40,7 @@
#:use-module (gnu packages compression)
#:use-module (gnu packages cpio)
#:use-module (gnu packages file)
+ #:use-module (gnu packages gawk)
#:use-module (gnu packages java)
#:use-module (gnu packages linux)
#:use-module (gnu packages machine-learning)
@@ -1690,7 +1691,7 @@ sequencing tag position and orientation.")
(define-public mafft
(package
(name "mafft")
- (version "7.221")
+ (version "7.267")
(source (origin
(method url-fetch)
(uri (string-append
@@ -1699,7 +1700,7 @@ sequencing tag position and orientation.")
(file-name (string-append name "-" version ".tgz"))
(sha256
(base32
- "0xi7klbsgi049vsrk6jiwh9wfj3b770gz3c8c7zwij448v0dr73d"))))
+ "1xl6xq1rfxkws0svrlhyqxhhwbv6r77jwblsdpcyiwzsscw6wlk0"))))
(build-system gnu-build-system)
(arguments
`(#: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
(("^SCRIPTS = mafft mafft-homologs.rb")
"SCRIPTS = mafft")
+ ;; remove mafft-homologs from MANPAGES
+ (("^MANPAGES = mafft.1 mafft-homologs.1")
+ "MANPAGES = mafft.1")
;; remove mafft-distance from PROGS
(("^PROGS = dvtditr dndfast7 dndblast sextet5 mafft-distance")
"PROGS = dvtditr dndfast7 dndblast sextet5")
@@ -1732,9 +1736,22 @@ sequencing tag position and orientation.")
(("^\t\\$\\(INSTALL\\) -m 644 \\$\\(MANPAGES\\) \
\\$\\(DESTDIR\\)\\$\\(LIBDIR\\)") "#"))
#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))))
(inputs
- `(("perl" ,perl)))
+ `(("perl" ,perl)
+ ("gawk" ,gawk)
+ ("grep" ,grep)))
+ (propagated-inputs
+ `(("coreutils" ,coreutils)))
(home-page "http://mafft.cbrc.jp/alignment/software/")
(synopsis "Multiple sequence alignment program")
(description