From mboxrd@z Thu Jan 1 00:00:00 1970 From: Ricardo Wurmus Subject: Re: [PATCH] Add vcflib. Date: Wed, 20 Apr 2016 14:46:21 +0200 Message-ID: References: <878u1aa62m.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]:55460) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1asrWa-0003mL-By for guix-devel@gnu.org; Wed, 20 Apr 2016 08:46:33 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1asrWX-00024r-0U for guix-devel@gnu.org; Wed, 20 Apr 2016 08:46:32 -0400 In-Reply-To: <878u1aa62m.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 dfc9b373bbce0f36882407cec47440a0a44c78d1 Mon Sep 17 00:00:00 2001 > From: Roel Janssen > Date: Tue, 22 Mar 2016 14:59:05 +0100 > Subject: [PATCH 1/8] gnu: Add tabixpp. > * gnu/packages/bioinformatics.scm (tabixpp): New variable. > --- > gnu/packages/bioinformatics.scm | 39 +++++++++++++++++++++++++++++++++= ++++++ > 1 file changed, 39 insertions(+) > diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformat= ics.scm > index 281bd1f..6792be9 100644 > --- a/gnu/packages/bioinformatics.scm > +++ b/gnu/packages/bioinformatics.scm > @@ -4791,3 +4791,42 @@ negative binomial distribution to model the read= counts among the samples in > the same group, and look for consistent differences between ChIP and c= ontrol > group or two ChIP groups run under different conditions.") > (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) > + (inputs > + `(("htslib" ,htslib) > + ("zlib" ,zlib))) > + (arguments > + `(#:tests? #f ; There are no tests to run. > + #:phases > + (modify-phases %standard-phases > + (delete 'configure) ; There is no configure phase. > + ;; Modify the build phase to use the separately packaged htsli= b. > + (replace 'build > + (lambda* (#:key inputs #:allow-other-keys) > + (let ((htslib-ref (assoc-ref inputs "htslib"))) > + (zero? > + (system* "make" > + (string-append "HTS_LIB=3D" htslib-ref "/lib/libhts.a= ") > + "HTS_HEADERS=3D" ; Do not check for local htslib head= ers. > + (string-append "LIBPATH=3D-L. -L" htslib-ref > "/include")))))) Is this really necessary or could you use make-flags instead? That would be the preferred way of doing this rather than replacing the build phase. > + (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") =E2=80=9Ctabix=E2=80=9D or =E2=80=9CTabix=E2=80=9D? > + (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))) =E2=80=9Ctabix=E2=80=9D or =E2=80=9CTabix=E2=80=9D? Could you please send an updated patch? ~~ Ricardo