From mboxrd@z Thu Jan 1 00:00:00 1970 From: Ricardo Wurmus Subject: [PATCH] gnu: Add CLIPper. Date: Thu, 26 Feb 2015 15:13:09 +0100 Message-ID: Mime-Version: 1.0 Content-Type: text/x-patch Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:40873) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1YQzBr-0002yM-AI for guix-devel@gnu.org; Thu, 26 Feb 2015 09:13:29 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1YQzBm-0001LU-5v for guix-devel@gnu.org; Thu, 26 Feb 2015 09:13:23 -0500 Received: from sinope.bbbm.mdc-berlin.de ([141.80.25.23]:34703) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1YQzBl-0001Kw-N1 for guix-devel@gnu.org; Thu, 26 Feb 2015 09:13:18 -0500 Received: from localhost (localhost [127.0.0.1]) by sinope.bbbm.mdc-berlin.de (Postfix) with ESMTP id 1B539280863 for ; Thu, 26 Feb 2015 15:13:16 +0100 (CET) Received: from sinope.bbbm.mdc-berlin.de ([127.0.0.1]) by localhost (sinope.bbbm.mdc-berlin.de [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id iys0WNueDPdn for ; Thu, 26 Feb 2015 15:13:10 +0100 (CET) Received: from HTCATWO.mdc-berlin.net (puck.citx.mdc-berlin.de [141.80.36.101]) by sinope.bbbm.mdc-berlin.de (Postfix) with ESMTP for ; Thu, 26 Feb 2015 15:13:10 +0100 (CET) Content-Disposition: inline; filename="0001-gnu-Add-CLIPper.patch" 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-bounces+gcggd-guix-devel=m.gmane.org@gnu.org To: Guix-devel >From 894c295fe9437987ed5d447c3122045a73259bc1 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 25 Feb 2015 16:38:17 +0100 Subject: [PATCH] gnu: Add CLIPper. * gnu/packages/bioinformatics.scm (clipper): New variable. --- gnu/packages/bioinformatics.scm | 38 ++++++++++++++++++++++++++++++++++++++ 1 file changed, 38 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index a425f61..b08e133 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -235,6 +235,44 @@ gapped, local, and paired-end alignment modes.") (supported-systems '("x86_64-linux")) (license license:gpl3+))) +(define-public clipper + (package + (name "clipper") + (version "0.3.0") + (source (origin + (method url-fetch) + (uri (string-append + "https://github.com/YeoLab/clipper/archive/" + version ".tar.gz")) + (sha256 + (base32 + "1q7jpimsqln7ic44i8v2rx2haj5wvik8hc1s2syd31zcn0xk1iyq")) + (modules '((guix build utils))) + (snippet + ;; remove unnecessary setup dependency + '(substitute* "setup.py" + (("setup_requires = .*") ""))))) + (build-system python-build-system) + (arguments `(#:python ,python-2)) ; only Python 2 is supported + (inputs + `(("htseq" ,htseq) + ("python-pybedtools" ,python2-pybedtools) + ("python-cython" ,python2-cython) + ("python-scikit-learn" ,python2-scikit-learn) + ("python-matplotlib" ,python2-matplotlib) + ("python-pysam" ,python2-pysam) + ("python-numpy" ,python2-numpy) + ("python-scipy" ,python2-scipy))) + (native-inputs + `(("python-mock" ,python2-mock) ; for tests + ("python-pytz" ,python2-pytz) ; for tests + ("python-setuptools" ,python2-setuptools))) + (home-page "https://github.com/YeoLab/clipper") + (synopsis "CLIP peak enrichment recognition") + (description + "CLIPper is a tool to define peaks in CLIP-seq datasets.") + (license license:gpl2))) + (define-public flexbar (package (name "flexbar") -- 2.1.0