From mboxrd@z Thu Jan 1 00:00:00 1970 From: Ricardo Wurmus Subject: Re: [PATCH] Add vcflib. Date: Mon, 16 Jan 2017 22:59:57 +0100 Message-ID: <87shoi8y3m.fsf@mdc-berlin.de> References: <878u1aa62m.fsf@gnu.org> <878u06hzqu.fsf@gnu.org> <87d1pcxoob.fsf@gnu.org> Mime-Version: 1.0 Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: quoted-printable Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:34284) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1cTFK1-0000Bc-2l for guix-devel@gnu.org; Mon, 16 Jan 2017 17:00:14 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1cTFJx-00086M-UL for guix-devel@gnu.org; Mon, 16 Jan 2017 17:00:13 -0500 In-Reply-To: <87d1pcxoob.fsf@gnu.org> 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: Roel Janssen Cc: guix-devel@gnu.org Roel Janssen writes: > 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/bioinformat= ics.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 con= ditions.") > (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=3D" ; Do not check for local htslib= headers. > + ,(string-append "HTS_LIB=3D" htslib-ref "/lib/li= bhts.a") > + ,(string-append "LIBPATH=3D-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))) One more from the bottom of my inbox at work=E2=80=A6 (I haven=E2=80=99t= even started looking at my private inbox.) Please add =E2=80=9C#t=E2=80=9D to the end of the =E2=80=9Cinstall=E2=80=9D= phase and adjust the indentation of the make-flags. The rest looks good. Thanks! -- Ricardo