From mboxrd@z Thu Jan 1 00:00:00 1970 From: Ricardo Wurmus Subject: [PATCH] Add idr. Date: Tue, 16 Jun 2015 11:37:28 +0200 Message-ID: Mime-Version: 1.0 Content-Type: text/x-patch Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:58730) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1Z4nJP-0001za-2H for guix-devel@gnu.org; Tue, 16 Jun 2015 05:37:47 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1Z4nJK-0006Ga-SI for guix-devel@gnu.org; Tue, 16 Jun 2015 05:37:43 -0400 Received: from sinope.bbbm.mdc-berlin.de ([141.80.25.23]:37413) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1Z4nJK-0006E9-9Z for guix-devel@gnu.org; Tue, 16 Jun 2015 05:37:38 -0400 Received: from localhost (localhost [127.0.0.1]) by sinope.bbbm.mdc-berlin.de (Postfix) with ESMTP id B3C6E280844 for ; Tue, 16 Jun 2015 11:37:35 +0200 (CEST) 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 Kievpc4x5uYJ for ; Tue, 16 Jun 2015 11:37:29 +0200 (CEST) Received: from HTCAONE.mdc-berlin.net (mab.citx.mdc-berlin.de [141.80.36.102]) by sinope.bbbm.mdc-berlin.de (Postfix) with ESMTP for ; Tue, 16 Jun 2015 11:37:29 +0200 (CEST) Content-Disposition: inline; filename="0001-gnu-Add-idr.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 815a5e24f43f61c4beb243d98beb0659bbd74b3a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 16 Jun 2015 11:33:26 +0200 Subject: [PATCH] gnu: Add idr. * gnu/packages/bioinformatics.scm (idr): New variable. --- gnu/packages/bioinformatics.scm | 40 ++++++++++++++++++++++++++++++++++++++++ 1 file changed, 40 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index eb15d40..ac4c50d 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1061,6 +1061,46 @@ data. It also provides the bgzip, htsfile, and tabix utilities.") ;; the rest is released under the Expat license (license (list license:expat license:bsd-3)))) +(define-public idr + (package + (name "idr") + (version "2.0.0") + (source (origin + (method url-fetch) + (uri (string-append + "https://github.com/nboley/idr/archive/" + version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "1k3x44biak00aiv3hpm1yd6nn4hhp7n0qnbs3zh2q9sw7qr1qj5r")))) + (build-system python-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after + 'install 'wrap-program + (lambda* (#:key outputs #:allow-other-keys) + (let ((out (assoc-ref %outputs "out")) + (path (getenv "PYTHONPATH"))) + (wrap-program (string-append out "/bin/idr") + `("PYTHONPATH" ":" prefix (,path)))) + #t))))) + (inputs + `(("python-scipy" ,python-scipy) + ("python-numpy" ,python-numpy) + ("python-matplotlib" ,python-matplotlib))) + (native-inputs + `(("python-cython" ,python-cython) + ("python-setuptools" ,python-setuptools))) + (home-page "https://github.com/nboley/idr") + (synopsis "Tool to measure the irreproducible discovery rate (IDR)") + (description + "The IDR (Irreproducible Discovery Rate) framework is a unified approach +to measure the reproducibility of findings identified from replicate +experiments and provide highly stable thresholds based on reproducibility.") + (license license:gpl3+))) + (define-public macs (package (name "macs") -- 2.1.0