From patchwork Mon Jan 20 12:18:30 2020 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Patchwork-Submitter: Roel Janssen X-Patchwork-Id: 19922 Return-Path: X-Original-To: patchwork@mira.cbaines.net Delivered-To: patchwork@mira.cbaines.net Received: by mira.cbaines.net (Postfix, from userid 113) id 8734417AE0; Mon, 20 Jan 2020 12:19:15 +0000 (GMT) X-Spam-Checker-Version: SpamAssassin 3.4.0 (2014-02-07) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-1.9 required=5.0 tests=BAYES_00,URIBL_BLOCKED autolearn=unavailable autolearn_force=no version=3.4.0 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTP id 62ADA17ADF for ; Mon, 20 Jan 2020 12:19:11 +0000 (GMT) Received: from localhost ([::1]:35402 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1itW1O-0004CS-Rw for patchwork@mira.cbaines.net; Mon, 20 Jan 2020 07:19:10 -0500 Received: from eggs.gnu.org ([2001:470:142:3::10]:52413) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1itW1H-0004C6-CJ for guix-patches@gnu.org; Mon, 20 Jan 2020 07:19:04 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1itW1G-0005di-0l for guix-patches@gnu.org; Mon, 20 Jan 2020 07:19:03 -0500 Received: from debbugs.gnu.org ([209.51.188.43]:38490) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1itW1F-0005ci-SV for guix-patches@gnu.org; Mon, 20 Jan 2020 07:19:01 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1itW1F-00070Z-OR for guix-patches@gnu.org; Mon, 20 Jan 2020 07:19:01 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#39201] [PATCH] gnu: Add r-deconstructsigs. Resent-From: Roel Janssen Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Mon, 20 Jan 2020 12:19:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 39201 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 39201@debbugs.gnu.org X-Debbugs-Original-To: guix-patches@gnu.org Received: via spool by submit@debbugs.gnu.org id=B.157952272626914 (code B ref -1); Mon, 20 Jan 2020 12:19:01 +0000 Received: (at submit) by debbugs.gnu.org; 20 Jan 2020 12:18:46 +0000 Received: from localhost ([127.0.0.1]:44463 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1itW0w-0006zu-K8 for submit@debbugs.gnu.org; Mon, 20 Jan 2020 07:18:46 -0500 Received: from lists.gnu.org ([209.51.188.17]:51011) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1itW0p-0006zT-Oz for submit@debbugs.gnu.org; Mon, 20 Jan 2020 07:18:39 -0500 Received: from eggs.gnu.org ([2001:470:142:3::10]:52357) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1itW0o-0004AJ-94 for guix-patches@gnu.org; Mon, 20 Jan 2020 07:18:35 -0500 Received: from fencepost.gnu.org ([2001:470:142:3::e]:50408) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1itW0o-00042X-3X for guix-patches@gnu.org; Mon, 20 Jan 2020 07:18:34 -0500 Received: from [143.121.198.62] (port=55384 helo=cog147) by fencepost.gnu.org with esmtpsa (TLS1.2:RSA_AES_256_CBC_SHA1:256) (Exim 4.82) (envelope-from ) id 1itW0m-0004Fc-Uw for guix-patches@gnu.org; Mon, 20 Jan 2020 07:18:33 -0500 Message-ID: <5d8aa06a6dd9845acfab5685b4106e7c382a7887.camel@gnu.org> From: Roel Janssen Date: Mon, 20 Jan 2020 13:18:30 +0100 X-Mailer: Evolution 3.28.5-0ubuntu0.18.04.1 Mime-Version: 1.0 X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] X-Received-From: 209.51.188.43 X-BeenThere: guix-patches@gnu.org List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org Sender: "Guix-patches" X-getmail-retrieved-from-mailbox: Patches Dear Guix, Here's a patch to add r-deconstructsigs. I added it to the cran module because that's where it originates from, but it takes a reference genome from bioconductor. So I had to use the bioconductor module. Is that OK? Thanks for your hard work and valuable time. Kind regards, Roel Janssen From e2a436698e81ce6b70be982a2193e6307606be41 Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Mon, 20 Jan 2020 13:14:52 +0100 Subject: [PATCH] gnu: Add r-deconstructsigs. * gnu/packages/cran.scm (r-deconstructsigs): New variable. --- gnu/packages/cran.scm | 29 ++++++++++++++++++++++++++++- 1 file changed, 28 insertions(+), 1 deletion(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index ff2490bc31..f4ecb9dec7 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -2,7 +2,7 @@ ;;; Copyright © 2015, 2016, 2017, 2018, 2019, 2020 Ricardo Wurmus ;;; Copyright © 2015 Andreas Enge ;;; Copyright © 2016, 2017 Ben Woodcroft -;;; Copyright © 2016, 2017, 2018 Roel Janssen +;;; Copyright © 2016, 2017, 2018, 2020 Roel Janssen ;;; Copyright © 2017, 2018, 2019 Tobias Geerinckx-Rice ;;; Copyright © 2017 Raoul Bonnal ;;; Copyright © 2018 Vijayalakshmi Vedantham @@ -43,6 +43,7 @@ #:use-module (guix build-system r) #:use-module (gnu packages algebra) #:use-module (gnu packages base) + #:use-module (gnu packages bioconductor) #:use-module (gnu packages bioinformatics) #:use-module (gnu packages c) #:use-module (gnu packages compression) @@ -1911,6 +1912,32 @@ instructed to explore various modifications of the objects (e.g., sorting rows, dropping names) to see if the modified versions are identical.") (license license:gpl2+))) +(define-public r-deconstructsigs + (package + (name "r-deconstructsigs") + (version "1.8.0") + (source (origin + (method url-fetch) + (uri (cran-uri "deconstructSigs" version)) + (sha256 + (base32 + "014x0nb23jb98666kaav2phkvmkr38pi38jv0dqd4jv7zp0gdf1a")))) + (properties + `((upstream-name . "deconstructSigs"))) + (build-system r-build-system) + (propagated-inputs + `(("r-bsgenome" ,r-bsgenome) + ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-reshape2" ,r-reshape2))) + (home-page "https://github.com/raerose01/deconstructSigs") + (synopsis "Identifies signatures present in a tumor sample") + (description "This package takes sample information in the form of the +fraction of mutations in each of 96 trinucleotide contexts and identifies +the weighted combination of published signatures that, when summed, most +closely reconstructs the mutational profile.") + (license license:gpl2+))) + (define-public r-dendextend (package (name "r-dendextend") -- 2.17.1