From: Roel Janssen <roel@gnu.org>
To: guix-devel@gnu.org
Subject: [PATCH] gnu: vcftools: Update to 0.1.14.
Date: Mon, 04 Apr 2016 14:12:05 +0200 [thread overview]
Message-ID: <8760vxd14a.fsf@gnu.org> (raw)
[-- Warning: decoded text below may be mangled, UTF-8 assumed --]
[-- Attachment #1: 0001-gnu-vcftools-Update-to-0.1.14.patch --]
[-- Type: text/x-patch, Size: 3071 bytes --]
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
[-- Attachment #2: Type: text/plain, Size: 350 bytes --]
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
next reply other threads:[~2016-04-04 12:11 UTC|newest]
Thread overview: 5+ messages / expand[flat|nested] mbox.gz Atom feed top
2016-04-04 12:12 Roel Janssen [this message]
2016-04-04 17:28 ` [PATCH] gnu: vcftools: Update to 0.1.14 Alex Kost
2016-04-04 18:05 ` Roel Janssen
2016-04-05 8:51 ` Alex Kost
2016-04-05 9:15 ` Roel Janssen
Reply instructions:
You may reply publicly to this message via plain-text email
using any one of the following methods:
* Save the following mbox file, import it into your mail client,
and reply-to-all from there: mbox
Avoid top-posting and favor interleaved quoting:
https://en.wikipedia.org/wiki/Posting_style#Interleaved_style
List information: https://guix.gnu.org/
* Reply using the --to, --cc, and --in-reply-to
switches of git-send-email(1):
git send-email \
--in-reply-to=8760vxd14a.fsf@gnu.org \
--to=roel@gnu.org \
--cc=guix-devel@gnu.org \
/path/to/YOUR_REPLY
https://kernel.org/pub/software/scm/git/docs/git-send-email.html
* If your mail client supports setting the In-Reply-To header
via mailto: links, try the mailto: link
Be sure your reply has a Subject: header at the top and a blank line
before the message body.
Code repositories for project(s) associated with this public inbox
https://git.savannah.gnu.org/cgit/guix.git
This is a public inbox, see mirroring instructions
for how to clone and mirror all data and code used for this inbox;
as well as URLs for read-only IMAP folder(s) and NNTP newsgroup(s).