From mboxrd@z Thu Jan 1 00:00:00 1970 From: Ricardo Wurmus Subject: Re: [PATCH] Add vcflib. Date: Tue, 26 Apr 2016 16:47:09 +0200 Message-ID: References: <878u1aa62m.fsf@gnu.org> <878u06hzqu.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]:33792) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1av4Gl-0006d9-Pu for guix-devel@gnu.org; Tue, 26 Apr 2016 10:47:20 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1av4Gi-0002Sz-Jg for guix-devel@gnu.org; Tue, 26 Apr 2016 10:47:19 -0400 In-Reply-To: <878u06hzqu.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: > Hello Ricardo, > > Thank you for your review. > > Ricardo Wurmus writes: > >> Roel Janssen writes: >>> From dfc9b373bbce0f36882407cec47440a0a44c78d1 Mon Sep 17 00:00:00 200= 1 >>> 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/bioinform= atics.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 re= ad counts among the samples in >>> the same group, and look for consistent differences between ChIP and= control >>> 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 hts= lib. >>> + (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 he= aders. >>> + (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 bui= ld >> phase. > > So I had tried, but my Scheme skills failed there. > In the new patch I used make-flags instead. I hope the (let ...) is > appropriate there. I like it because it allows me to stay within 80 > columns, and avoid repetitive (assoc-ref %build-inputs "htslib"). > >>> + (replace 'install >>> + (lambda* (#:key outputs #:allow-other-keys) >>> + (let ((bin (string-append (assoc-ref outputs "out") "/bi= n"))) >>> + (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? > > Tabix I suppose. > >>> + (description "This is a C++ wrapper around the Tabix project whic= h 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? > > Right. I changed both occurrences to =E2=80=9CTabix=E2=80=9D. > >> 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? ~~ Ricardo