From mboxrd@z Thu Jan 1 00:00:00 1970 From: Ricardo Wurmus Subject: Re: [PATCH] Add vcflib. Date: Mon, 16 Jan 2017 22:54:57 +0100 Message-ID: <87vate8yby.fsf@mdc-berlin.de> References: <878u1aa62m.fsf@gnu.org> <87a8kgxnsg.fsf@gnu.org> <878u00xnqz.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]:33333) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1cTFFN-0006Uw-QM for guix-devel@gnu.org; Mon, 16 Jan 2017 16:55:26 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1cTFFK-0006cE-Kg for guix-devel@gnu.org; Mon, 16 Jan 2017 16:55:25 -0500 In-Reply-To: <878u00xnqz.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 98ed1adae91aca2c118779f5333dc21446f1c720 Mon Sep 17 00:00:00 2001 > From: Roel Janssen > Date: Tue, 26 Apr 2016 19:48:31 +0200 > Subject: [PATCH] gnu: Add intervaltree. > > * gnu/packages/bioinformatics.scm (intervaltree): New variable. > --- > gnu/packages/bioinformatics.scm | 32 ++++++++++++++++++++++++++++++++ > 1 file changed, 32 insertions(+) > > diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformat= ics.scm > index 620439f..9ad6c38 100644 > --- a/gnu/packages/bioinformatics.scm > +++ b/gnu/packages/bioinformatics.scm > @@ -885,6 +885,38 @@ well as many of the command line options.") > multiple sequence alignments.") > (license license:expat))) > =20 > +(define-public intervaltree > + (let ((commit "dbb4c513d1ad3baac516fc1484c995daf9b42838")) > + (package > + (name "intervaltree") > + (version (string-append "0-1." (string-take commit 7))) > + (source (origin > + (method url-fetch) > + (uri (string-append "https://github.com/ekg/intervaltree/archi= ve/" > + commit ".tar.gz")) > + (file-name (string-append name "-" version ".tar.gz")) > + (sha256 > + (base32 "19prwpn2wxsrijp5svfqvfcxl5nj7zdhm3jycd5kqhl9nifpmcks= ")))) > + (build-system gnu-build-system) > + (arguments > + `(#:phases > + (modify-phases %standard-phases > + (delete 'configure) ; There is no configure phase. > + (replace 'check > + (lambda _ > + (zero? (system* "./interval_tree_test")))) > + (replace 'install > + (lambda* (#:key outputs #:allow-other-keys) > + (let ((include (string-append (assoc-ref outputs "out") > + "/include/intervaltree"))= ) > + (install-file "IntervalTree.h" include))))))) > + (home-page "https://github.com/ekg/intervaltree/") > + (synopsis "Minimal C++ interval tree implementation") > + (description "This library provides a basic implementation of an= interval > +tree using C++ templates, allowing the insertion of arbitrary types in= to the > +tree.") > + (license license:expat)))) > + > (define-public python-pysam > (package > (name "python-pysam") That=E2=80=99s a nice patch that doesn=E2=80=99t seem to be in Guix yet. = It was part of your vcflib series, but it never made it upstream. Would you like to rebase and push it? --=20 Ricardo