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gnu: vcftools: Update to 0.1.14.

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* gnu/packages/bioinformatics.scm (vcftools): Update to 0.1.14.
[arguments]: Do not modify phases as it is not needed anymore.
[native-inputs]: Add 'pkg-config'.
[home-page]: Update to new location.

Signed-off-by: Alex Kost <alezost@gmail.com>
This commit is contained in:
Roel Janssen 2016-04-04 20:04:48 +02:00 committed by Alex Kost
parent 17130e3919
commit 9b36e25607
1 changed files with 9 additions and 14 deletions
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23
gnu/packages/bioinformatics.scm
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@ -3692,15 +3692,15 @@ (define-public stringtie
(define-public vcftools (define-public vcftools
(package (package
(name "vcftools") (name "vcftools")
(version "0.1.12b") (version "0.1.14")
(source (origin (source (origin
(method url-fetch) (method url-fetch)
(uri (string-append (uri (string-append
"mirror://sourceforge/vcftools/vcftools_" "https://github.com/vcftools/vcftools/releases/download/v"
version ".tar.gz")) version "/vcftools-" version ".tar.gz"))
(sha256 (sha256
(base32 (base32
"148al9h7f8g8my2qdnpax51kdd2yjrivlx6frvakf4lz5r8j88wx")))) "10l5c07z9p4i9pr4gl54b2c9h6ndhqlbq1rashg2zcgwkbfrkmvn"))))
(build-system gnu-build-system) (build-system gnu-build-system)
(arguments (arguments
`(#:tests? #f ; no "check" target `(#:tests? #f ; no "check" target
@ -3708,18 +3708,13 @@ (define-public vcftools
"CFLAGS=-O2" ; override "-m64" flag "CFLAGS=-O2" ; override "-m64" flag
(string-append "PREFIX=" (assoc-ref %outputs "out")) (string-append "PREFIX=" (assoc-ref %outputs "out"))
(string-append "MANDIR=" (assoc-ref %outputs "out") (string-append "MANDIR=" (assoc-ref %outputs "out")
"/share/man/man1")) "/share/man/man1"))))
#:phases (native-inputs
(alist-cons-after `(("pkg-config" ,pkg-config)))
'unpack 'patch-manpage-install
(lambda _
(substitute* "Makefile"
(("cp \\$\\{PREFIX\\}/cpp/vcftools.1") "cp ./cpp/vcftools.1")))
(alist-delete 'configure %standard-phases))))
(inputs (inputs
`(("perl" ,perl) `(("perl" ,perl)
("zlib" ,zlib))) ("zlib" ,zlib)))
(home-page "http://vcftools.sourceforge.net/") (home-page "https://vcftools.github.io/")
(synopsis "Tools for working with VCF files") (synopsis "Tools for working with VCF files")
(description (description
"VCFtools is a program package designed for working with VCF files, such "VCFtools is a program package designed for working with VCF files, such
@ -3727,7 +3722,7 @@ (define-public vcftools
provide easily accessible methods for working with complex genetic variation provide easily accessible methods for working with complex genetic variation
data in the form of VCF files.") data in the form of VCF files.")
;; The license is declared as LGPLv3 in the README and ;; The license is declared as LGPLv3 in the README and
;; at http://vcftools.sourceforge.net/license.html ;; at https://vcftools.github.io/license.html
(license license:lgpl3))) (license license:lgpl3)))
(define-public vsearch (define-public vsearch