From fc68a4593db1449bb8d55a4d8edee0a0fd05ee64 Mon Sep 17 00:00:00 2001
From: Roel Janssen <roel@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