From mboxrd@z Thu Jan 1 00:00:00 1970 From: Roel Janssen Subject: [PATCH] gnu: vcftools: Update to 0.1.14. Date: Mon, 04 Apr 2016 14:12:05 +0200 Message-ID: <8760vxd14a.fsf@gnu.org> Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="=-=-=" Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:39887) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1an3MG-0004s6-82 for guix-devel@gnu.org; Mon, 04 Apr 2016 08:11:53 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1an3MC-0005ad-LS for guix-devel@gnu.org; Mon, 04 Apr 2016 08:11:52 -0400 Received: from fencepost.gnu.org ([2001:4830:134:3::e]:45190) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1an3MC-0005aT-Ia for guix-devel@gnu.org; Mon, 04 Apr 2016 08:11:48 -0400 Received: from [143.121.239.252] (port=45710 helo=roel-tp) by fencepost.gnu.org with esmtpsa (TLS1.2:RSA_AES_128_CBC_SHA1:128) (Exim 4.82) (envelope-from ) id 1an3MC-0002p3-1e for guix-devel@gnu.org; Mon, 04 Apr 2016 08:11:48 -0400 List-Id: "Development of GNU Guix and the GNU System distribution." List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-devel-bounces+gcggd-guix-devel=m.gmane.org@gnu.org Sender: guix-devel-bounces+gcggd-guix-devel=m.gmane.org@gnu.org To: guix-devel@gnu.org --=-=-= Content-Type: text/x-patch Content-Disposition: attachment; filename=0001-gnu-vcftools-Update-to-0.1.14.patch >From fc68a4593db1449bb8d55a4d8edee0a0fd05ee64 Mon Sep 17 00:00:00 2001 From: Roel Janssen 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 --=-=-= Content-Type: text/plain 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 --=-=-=--