>From fc68a4593db1449bb8d55a4d8edee0a0fd05ee64 Mon Sep 17 00:00:00 2001
From: Roel Janssen <r...@gnu.org>
Date: Mon, 4 Apr 2016 14:06:33 +0200
Subject: [PATCH] gnu: vcftools: Update to 0.1.14.
* gnu/packages/bioinformatics.scm (vcftools): Update to 0.1.14.
[home-page]: Update to new homepage.
---
gnu/packages/bioinformatics.scm | 29 ++++++++++++++++++-----------
1 file changed, 18 insertions(+), 11 deletions(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 250deb9..ff8d961 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -3692,15 +3692,15 @@ Cuffdiff or Ballgown programs.")
(define-public vcftools
(package
(name "vcftools")
- (version "0.1.12b")
+ (version "0.1.14")
(source (origin
(method url-fetch)
(uri (string-append
- "mirror://sourceforge/vcftools/vcftools_"
+ "https://github.com/vcftools/vcftools/archive/v";
version ".tar.gz"))
(sha256
(base32
- "148al9h7f8g8my2qdnpax51kdd2yjrivlx6frvakf4lz5r8j88wx"))))
+ "1pvgv9vzlgny5h3ljcy7fl2iyn98v366kdxnxv0h36aycj20ai5s"))))
(build-system gnu-build-system)
(arguments
`(#:tests? #f ; no "check" target
@@ -3710,16 +3710,23 @@ Cuffdiff or Ballgown programs.")
(string-append "MANDIR=" (assoc-ref %outputs "out")
"/share/man/man1"))
#:phases
- (alist-cons-after
- 'unpack 'patch-manpage-install
- (lambda _
- (substitute* "Makefile"
- (("cp \\$\\{PREFIX\\}/cpp/vcftools.1") "cp ./cpp/vcftools.1")))
- (alist-delete 'configure %standard-phases))))
+ (modify-phases %standard-phases
+ (add-after 'configure 'patch-manpage-install
+ (lambda _
+ (substitute* "Makefile"
+ (("cp \\$\\{PREFIX\\}/cpp/vcftools.1") "cp ./cpp/vcftools.1"))))
+ (add-before 'configure 'run-autogen
+ (lambda _
+ (zero? (system* "sh" "autogen.sh")))))))
+ (native-inputs
+ `(("autoconf" ,(autoconf-wrapper))
+ ("automake" ,automake)
+ ("libtool" ,libtool)
+ ("pkg-config" ,pkg-config)))
(inputs
`(("perl" ,perl)
("zlib" ,zlib)))
- (home-page "http://vcftools.sourceforge.net/";)
+ (home-page "https://vcftools.github.io/";)
(synopsis "Tools for working with VCF files")
(description
"VCFtools is a program package designed for working with VCF files, such
@@ -3727,7 +3734,7 @@ as those generated by the 1000 Genomes Project. The aim of VCFtools is to
provide easily accessible methods for working with complex genetic variation
data in the form of VCF files.")
;; The license is declared as LGPLv3 in the README and
- ;; at http://vcftools.sourceforge.net/license.html
+ ;; at https://github.com/vcftools/vcftools/blob/master/README.md
(license license:lgpl3)))
(define-public vsearch
--
2.5.5
Dear Guix,
I would like to update 'vcftools' to 0.1.14 (the latest release).
The project now uses Autotools, so the configure phase should be run.
In addition to that, I had to run autogen.sh to generate a configure
script.
They moved from Sourceforge to Github, so I updated the source link and
the homepage to Github.
Kind regards,
Roel Janssen
