From mboxrd@z Thu Jan 1 00:00:00 1970 From: Roel Janssen Subject: Re: [PATCH] Add vcflib. Date: Tue, 26 Apr 2016 19:31:00 +0200 Message-ID: <87d1pcxoob.fsf@gnu.org> References: <878u1aa62m.fsf@gnu.org> <878u06hzqu.fsf@gnu.org> Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="=-=-=" Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:60168) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1av6pW-0008DR-1W for guix-devel@gnu.org; Tue, 26 Apr 2016 13:31:27 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1av6pR-0002FS-F0 for guix-devel@gnu.org; Tue, 26 Apr 2016 13:31:21 -0400 In-reply-to: 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" To: Ricardo Wurmus Cc: guix-devel@gnu.org --=-=-= Content-Type: text/x-patch Content-Disposition: attachment; filename=0001-gnu-Add-tabixpp-v2.patch >From 5cc17f0ceca12998a658dcd3cfd7494b137274e1 Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Tue, 26 Apr 2016 19:28:54 +0200 Subject: [PATCH] gnu: Add tabixpp. * gnu/packages/bioinformatics.scm (tabixpp): New variable. --- gnu/packages/bioinformatics.scm | 34 ++++++++++++++++++++++++++++++++++ 1 file changed, 34 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 620439f..450d250 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -5102,3 +5102,37 @@ group or two ChIP groups run under different conditions.") (description "This program compares version strings. It intends to be a replacement for strverscmp.") (license license:gpl3+)))) + +(define-public tabixpp + (package + (name "tabixpp") + (version "1.0.0") + (source (origin + (method url-fetch) + (uri (string-append "https://github.com/ekg/tabixpp/archive/v" + version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 "1s0lgks7qlvlhvcjhi2wm18nnza1bwcnic44ij7z8wfg88h4ivwn")))) + (build-system gnu-build-system) + (arguments + `(#:tests? #f ; There are no tests to run. + #:make-flags (let ((htslib-ref (assoc-ref %build-inputs "htslib"))) + `("HTS_HEADERS=" ; Do not check for local htslib headers. + ,(string-append "HTS_LIB=" htslib-ref "/lib/libhts.a") + ,(string-append "LIBPATH=-L. -L" htslib-ref "/include"))) + #:phases + (modify-phases %standard-phases + (delete 'configure) ; There is no configure phase. + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let ((bin (string-append (assoc-ref outputs "out") "/bin"))) + (install-file "tabix" bin))))))) + (inputs + `(("htslib" ,htslib) + ("zlib" ,zlib))) + (home-page "https://github.com/ekg/tabixpp") + (synopsis "C++ wrapper around Tabix project") + (description "This is a C++ wrapper around the Tabix project which abstracts +some of the details of opening and jumping in Tabix-indexed files.") + (license license:expat))) -- 2.7.4 --=-=-= Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit Ricardo Wurmus writes: > Roel Janssen writes: > >> Hello Ricardo, >> >> Thank you for your review. >> >> Ricardo Wurmus writes: >>>> + (replace 'install >>>> + (lambda* (#:key outputs #:allow-other-keys) >>>> + (let ((bin (string-append (assoc-ref outputs "out") "/bin"))) >>>> + (install-file "tabix++" bin))))))) >>>> + (home-page "https://github.com/ekg/tabixpp") >>>> + (synopsis "C++ wrapper around tabix project") >>> >>> “tabix” or “Tabix”? >> >> Tabix I suppose. >> >>>> + (description "This is a C++ wrapper around the Tabix project which abstracts >>>> +some of the details of opening and jumping in tabix-indexed files.") >>>> + (license license:expat))) >>> >>> “tabix” or “Tabix”? >> >> Right. I changed both occurrences to “Tabix”. >> >>> Could you please send an updated patch? >> >> Here it is. > > Thanks, looks good, except for having the inputs before the arguments. > I tried to apply the patch to master but it failed. Could you please > rebase it onto master and resend? Attached a new patch with the inputs after arguments. Thanks! Kind regards, Roel Janssen --=-=-=--