From mboxrd@z Thu Jan 1 00:00:00 1970 From: Ricardo Wurmus Subject: [PATCH] gnu: Add MACS. Date: Thu, 26 Feb 2015 17:12:59 +0100 Message-ID: Mime-Version: 1.0 Content-Type: text/x-patch Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:37807) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1YR13q-0006Lj-Op for guix-devel@gnu.org; Thu, 26 Feb 2015 11:13:20 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1YR13j-0004SN-Bw for guix-devel@gnu.org; Thu, 26 Feb 2015 11:13:14 -0500 Received: from sinope.bbbm.mdc-berlin.de ([141.80.25.23]:35600) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1YR13j-0004S9-3A for guix-devel@gnu.org; Thu, 26 Feb 2015 11:13:07 -0500 Received: from localhost (localhost [127.0.0.1]) by sinope.bbbm.mdc-berlin.de (Postfix) with ESMTP id 46A8E28071E for ; Thu, 26 Feb 2015 17:13:06 +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 lYdP8I_7aT5H for ; Thu, 26 Feb 2015 17:12:59 +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 17:12:59 +0100 (CET) Content-Disposition: inline; filename="0001-gnu-Add-MACS.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 9c69ab1e5f1091e1f36d8ca7716c7c394d09e4c2 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 26 Feb 2015 17:10:39 +0100 Subject: [PATCH] gnu: Add MACS. * gnu/packages/bioinformatics.scm (macs): New variable. --- gnu/packages/bioinformatics.scm | 31 +++++++++++++++++++++++++++++++ 1 file changed, 31 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 749d0a0..0960329 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -448,6 +448,37 @@ particular, reads spanning multiple exons.") from high-throughput sequencing assays.") (license license:gpl3+))) +(define-public macs + (package + (name "macs") + (version "2.1.0.20140616") + (source (origin + (method url-fetch) + (uri (string-append + "https://pypi.python.org/packages/source/M/MACS2/MACS2-" + version ".tar.gz")) + (sha256 + (base32 + "11lmiw6avqhwn75sn59g4lfkrr2kk20r3rgfbx9xfqb8rg9mi2n6")))) + (build-system python-build-system) + (arguments + `(#:python ,python-2 ; only compatible with Python 2.7 + #:tests? #f)) ; no test target + (inputs + `(("python-numpy" ,python2-numpy))) + (native-inputs + `(("python-setuptools" ,python2-setuptools))) + (home-page "http://github.com/taoliu/MACS/") + (synopsis "Model based analysis for ChIP-Seq data") + (description + "MACS is an implementation of a ChIP-Seq analysis algorithm for +identifying transcript factor binding sites named Model-based Analysis of +ChIP-Seq (MACS). MACS captures the influence of genome complexity to evaluate +the significance of enriched ChIP regions and it improves the spatial +resolution of binding sites through combining the information of both +sequencing tag position and orientation.") + (license license:bsd-3))) + (define-public rseqc (package (name "rseqc") -- 2.1.0