Re: [PATCH] gnu: vcftools: Update to 0.1.14.

[Roel Janssen <roel@gnu.org>]

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From f0cc38ea5ed57018785cc20352165a7e2cd18d84 Mon Sep 17 00:00:00 2001
From: Roel Janssen <roel@gnu.org>
Date: Mon, 4 Apr 2016 20:04:48 +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 | 23 +++++++++--------------
 1 file changed, 9 insertions(+), 14 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 250deb9..0afc0a6 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_"
-                     version ".tar.gz"))
+                    "https://github.com/vcftools/vcftools/releases/download/v"
+                    version "/vcftools-" version ".tar.gz"))
               (sha256
                (base32
-                "148al9h7f8g8my2qdnpax51kdd2yjrivlx6frvakf4lz5r8j88wx"))))
+                "10l5c07z9p4i9pr4gl54b2c9h6ndhqlbq1rashg2zcgwkbfrkmvn"))))
     (build-system gnu-build-system)
     (arguments
      `(#:tests? #f ; no "check" target
@@ -3708,18 +3708,13 @@ Cuffdiff or Ballgown programs.")
                      "CFLAGS=-O2" ; override "-m64" flag
                      (string-append "PREFIX=" (assoc-ref %outputs "out"))
                      (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))))
+                                    "/share/man/man1"))))
+    (native-inputs
+     `(("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 +3722,7 @@ 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://vcftools.github.io/license.html
     (license license:lgpl3)))
 
 (define-public vsearch
-- 
2.5.5


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Dear Alex,

Thank you for your quick response.

Alex Kost writes:

> Roel Janssen (2016-04-04 15:12 +0300) wrote:
>
>> 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.
>
> It happens because you use a source code "snapshot":
>
>   https://github.com/vcftools/vcftools/archive/v0.1.14.tar.gz
>
> Such things never contain "configure".  But look at:
>
>   https://github.com/vcftools/vcftools/releases
>
> There is a real release (made with "make dist"):
>
>   https://github.com/vcftools/vcftools/releases/download/v0.1.14/vcftools-0.1.14.tar.gz
>
> It contains all the required stuff, so there is no need to use autotools
> and to run "autogen.sh".

I hadn't noticed the real release file.
It also seems that the manpage is installed correctly by default now, so
I removed the substitution.

The new patch is cleaner.

Kind regards,
Roel Janssen