From patchwork Mon Jan 20 19:32:56 2020 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Patchwork-Submitter: Roel Janssen X-Patchwork-Id: 19924 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 7302717ADD; Mon, 20 Jan 2020 19:34:12 +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 1129017AB4 for ; Mon, 20 Jan 2020 19:34:11 +0000 (GMT) Received: from localhost ([::1]:43402 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1itcoM-0001Ta-6y for patchwork@mira.cbaines.net; Mon, 20 Jan 2020 14:34:10 -0500 Received: from eggs.gnu.org ([2001:470:142:3::10]:36817) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1itcoF-0001QK-MQ for guix-patches@gnu.org; Mon, 20 Jan 2020 14:34:04 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1itcoE-0002od-FK for guix-patches@gnu.org; Mon, 20 Jan 2020 14:34:03 -0500 Received: from debbugs.gnu.org ([209.51.188.43]:40106) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1itcoE-0002oV-Cg for guix-patches@gnu.org; Mon, 20 Jan 2020 14:34:02 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1itcoE-0007d5-Ak for guix-patches@gnu.org; Mon, 20 Jan 2020 14:34:02 -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 19:34:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 39201 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: Ricardo Wurmus Cc: 39201@debbugs.gnu.org Received: via spool by 39201-submit@debbugs.gnu.org id=B39201.157954878929258 (code B ref 39201); Mon, 20 Jan 2020 19:34:02 +0000 Received: (at 39201) by debbugs.gnu.org; 20 Jan 2020 19:33:09 +0000 Received: from localhost ([127.0.0.1]:46079 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1itcnN-0007bq-15 for submit@debbugs.gnu.org; Mon, 20 Jan 2020 14:33:09 -0500 Received: from eggs.gnu.org ([209.51.188.92]:55898) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1itcnL-0007be-Gy for 39201@debbugs.gnu.org; Mon, 20 Jan 2020 14:33:08 -0500 Received: from fencepost.gnu.org ([2001:470:142:3::e]:59416) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1itcnG-0002MG-9j; Mon, 20 Jan 2020 14:33:02 -0500 Received: from 2001-1c02-0b03-a700-f532-4553-7f2a-9b68.cable.dynamic.v6.ziggo.nl ([2001:1c02:b03:a700:f532:4553:7f2a:9b68]:52570) by fencepost.gnu.org with esmtpsa (TLS1.2:RSA_AES_256_CBC_SHA1:256) (Exim 4.82) (envelope-from ) id 1itcnF-0005JV-QJ; Mon, 20 Jan 2020 14:33:02 -0500 Message-ID: From: Roel Janssen Date: Mon, 20 Jan 2020 20:32:56 +0100 In-Reply-To: <87h80qw9ml.fsf@elephly.net> References: <5d8aa06a6dd9845acfab5685b4106e7c382a7887.camel@gnu.org> <87h80qw9ml.fsf@elephly.net> User-Agent: Evolution 3.34.3 (3.34.3-1.fc31) 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 Hi Ricardo! On Mon, 2020-01-20 at 14:16 +0100, Ricardo Wurmus wrote: > Hi Roel, > > > 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? > > Please add the package to the bioconductor module instead and add a > comment above to explain why. (That’s what we’ve done for other > packages like this.) So I did. Thanks for pointing this out. I attached the new patch. Thanks Ricardo! Kind regards, Roel Janssen From 403a80754c3f53c29c4430cc5a537ee781cc9b1e Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Mon, 20 Jan 2020 20:21:09 +0100 Subject: [PATCH] gnu: Add r-deconstructsigs. * gnu/packages/bioconductor.scm (r-deconstructsigs): New variable. --- gnu/packages/bioconductor.scm | 28 ++++++++++++++++++++++++++++ 1 file changed, 28 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ef34b99649..d4194e8ec2 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -694,6 +694,34 @@ annotations.") "This is a manifest package for Illumina's EPIC methylation arrays.") (license license:artistic2.0))) +;; This is a CRAN package, but it depends on r-bsgenome-hsapiens-ucsc-hg19 +;; from Bioconductor. +(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-do-db (package (name "r-do-db") -- 2.25.0