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| author | Ben Woodcroft <donttrustben@gmail.com> | 2015-12-15 20:34:52 +1000 |
|---|---|---|
| committer | Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> | 2015-12-21 15:16:01 +0100 |
| commit | 02f35bb5a755984c9c419101d53f59f6274a0b8a (patch) | |
| tree | 78fcec156c6b335f106d2e46db37d92688052f85 /gnu/packages | |
| parent | 1ef3f91a702e19b01aff2e85b7ea2abe1f7579a1 (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')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 23 |
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 |