From mboxrd@z Thu Jan 1 00:00:00 1970 From: Roel Janssen Subject: Re: [PATCH] gnu: vcftools: Update to 0.1.14. Date: Mon, 04 Apr 2016 20:05:56 +0200 Message-ID: <87k2kdfdvf.fsf@gnu.org> References: <8760vxd14a.fsf@gnu.org> <87lh4tth9x.fsf@gmail.com> Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="=-=-=" Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:49254) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1an8sl-0003g3-Ex for guix-devel@gnu.org; Mon, 04 Apr 2016 14:05:48 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1an8sh-0007J1-0F for guix-devel@gnu.org; Mon, 04 Apr 2016 14:05:47 -0400 In-reply-to: <87lh4tth9x.fsf@gmail.com> 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: Alex Kost Cc: guix-devel@gnu.org --=-=-= Content-Type: text/x-patch Content-Disposition: attachment; filename=0001-gnu-vcftools-Update-to-0.1.14.patch >From f0cc38ea5ed57018785cc20352165a7e2cd18d84 Mon Sep 17 00:00:00 2001 From: Roel Janssen 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 --=-=-= Content-Type: text/plain 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 --=-=-=--