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Resent-From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Fri, 05 Mar 2021 01:22:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 46937 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: To: <46937@debbugs.gnu.org> Cc: rekado@elephly.net, =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmE=?= =?utf-8?b?yJljdQ==?= Received: via spool by 46937-submit@debbugs.gnu.org id=B46937.161490726821670 (code B ref 46937); Fri, 05 Mar 2021 01:22:02 +0000 Received: (at 46937) by debbugs.gnu.org; 5 Mar 2021 01:21:08 +0000 Received: from localhost ([127.0.0.1]:60668 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lHz9Q-0005dS-9N for submit@debbugs.gnu.org; Thu, 04 Mar 2021 20:21:08 -0500 Received: from b2062.mx.srv.dfn.de ([194.95.234.172]:47605) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lHz9N-0005cW-Qg for 46937@debbugs.gnu.org; Thu, 04 Mar 2021 20:21:06 -0500 Received: from localhost (localhost [127.0.0.1]) by b2062.mx.srv.dfn.de (Postfix) with ESMTP id 9995116011B; Fri, 5 Mar 2021 02:20:59 +0100 (CET) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-transfer-encoding:content-type:content-type:mime-version :references:in-reply-to:x-mailer:message-id:date:date:subject :subject:from:from:received:received:received; s=mdc; t= 1614907259; x=1616721660; bh=N0aMjs0YAqYMrHJ9JsRrnwWAL7Ka5GerCkZ rwcMHcgY=; b=aszju8YGDAzJVsje7MTYhUbrT/ao9DJFqM8TDnndpOygFXU6Rmm iC1Vvq8XK2oODjzBGluQXcwXr+k7vQ5YoU3zNMFkUyvrG1q7DrI5ZKg9JW6zYXTz pAVhkxxeXrIJLr+HVa9ubcqzK33/DTStZaW8oin/5P9kOG+xNbdF8LDM= Received: from b2062.mx.srv.dfn.de ([127.0.0.1]) by localhost (mgw4-tub.srv.dfn.de [127.0.0.1]) (amavisd-new, port 20134) with ESMTP id B9u_4Xuh87qY; Fri, 5 Mar 2021 02:20:59 +0100 (CET) Received: from SW-IT-P-EX4.mdc-berlin.net (mgw4.mdc-berlin.de [141.80.113.62]) by b2062.mx.srv.dfn.de (Postfix) with ESMTPS; Fri, 5 Mar 2021 02:20:59 +0100 (CET) Received: from Guix-Ubuntu18.04 (141.80.113.106) by SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) with Microsoft SMTP Server (version=TLS1_2, cipher=TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384) id 15.1.2176.2; Fri, 5 Mar 2021 02:20:58 +0100 From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Date: Fri, 5 Mar 2021 02:20:38 +0100 Message-ID: <20210305012039.15219-2-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.30.1 In-Reply-To: <20210305012039.15219-1-madalinionel.patrascu@mdc-berlin.de> References: <20210305012039.15219-1-madalinionel.patrascu@mdc-berlin.de> MIME-Version: 1.0 X-Originating-IP: [141.80.113.106] X-ClientProxiedBy: SW-IT-P-EX3.mdc-berlin.net (141.80.113.61) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3080-8.6.1012-26010.004 X-TM-AS-Result: No-10--4.104600-8.000000 X-TMASE-MatchedRID: FTxIpntvkVXRtBxlwMMWfD8Ckw9b/GFeTJDl9FKHbrnvrj2fROADidSQ QZwCn1OrWGH5wVAlhqF58gNAZ71WHYjRwo/Cjf7ifOaYwP8dcX5IvK4LrXs1aTcQcUZK1ILgedg e6osRC6g37vLQSViJKPharoQvMIWZUriXxFmUkHwBnSWdyp4eob/I3arxTrvirFjA6CZN1k3ukJ QjHbvwOZh97xQuugnjLb6XLHjqIvT7lPrMqaVmF4vqrlGw2G/k/BBU1WQWNfKYeMTPaAHLLWnNr fyaFzoAj8WQoLb8C5uhu8LBW5hICTpB6vA8GIIRXA16ExwD56wB/ULfnyF0r6BWLBsfseG+OZss O+6krjjF+KCpGE37CJsoi2XrUn/JmTDwp0zM3zoqtq5d3cxkNRqXnrxrKCOXrDM22rSqua19EeG YUYJeLIDDQrkx7TtWS9wbvUevNHux4fwawh+QBlPqmZ4ScCB+ssF9BB5AQNDRmi5vpEJjMwYiFV GJeB5u6Mfa6qKy6iI+O46LdUapZwroQfh7NkPlxUbkcyBaCqh+3BndfXUhXQ== X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--4.104600-8.000000 X-TMASE-Version: SMEX-14.0.0.3080-8.6.1012-26010.004 X-TM-SNTS-SMTP: 09E6BB5DB9BEEA4E9E08D2520D447126E88819EED59B06C8C337265C2C5D82542000:F X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list 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 * gnu/packages/bioconductor.scm (r-universalmotif): New variable. --- gnu/packages/bioconductor.scm | 53 ++++++++++++++++++++++++++++++++++- 1 file changed, 52 insertions(+), 1 deletion(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a4d97fad65..55a9b07509 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4,7 +4,7 @@ ;;; Copyright © 2017, 2018, 2019 Tobias Geerinckx-Rice ;;; Copyright © 2019, 2020 Simon Tournier ;;; Copyright © 2020 Peter Lo -;;; Copyright © 2020 Mădălin Ionel Patrașcu +;;; Copyright © 2020, 2021 Mădălin Ionel Patrașcu ;;; Copyright © 2020 Jakub Kądziołka ;;; ;;; This file is part of GNU Guix. @@ -7435,6 +7435,57 @@ data. This modified test allows for testing differential expression in qPCR data.") (license license:gpl2+))) +(define-public r-universalmotif + (package + (name "r-universalmotif") + (version "1.8.3") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "universalmotif" version)) + (sha256 + (base32 + "1ys2kbayc1rzv8nzi60208yfslm4kzynndfg7vw2n0c30dvzycrc")))) + (properties + `((upstream-name . "universalmotif"))) + (build-system r-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'fix-link + (lambda _ + (substitute* "src/Makevars" + (("/usr/bin/strip") (which "strip"))) + #t))))) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-biostrings" ,r-biostrings) + ("r-ggplot2" ,r-ggplot2) + ("r-ggseqlogo" ,r-ggseqlogo) + ("r-iranges" ,r-iranges) + ("r-mass" ,r-mass) + ("r-rcpp" ,r-rcpp) + ("r-rcppthread" ,r-rcppthread) + ("r-rdpack" ,r-rdpack) + ("r-rlang" ,r-rlang) + ("r-s4vectors" ,r-s4vectors) + ("r-yaml" ,r-yaml))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page + "https://bioconductor.org/packages/universalmotif/") + (synopsis + "Specific structures importer, modifier, and exporter for R") + (description + "This package allows importing most common @dfn{specific structure} +(motif) types into R for use by functions provided by other Bioconductor +motif-related packages. Motifs can be exported into most major motif formats +from various classes as defined by other Bioconductor packages. A suite of +motif and sequence manipulation and analysis functions are included, including +enrichment, comparison, P-value calculation, shuffling, trimming, higher-order +motifs, and others.") + (license license:gpl3))) + ;; This is a CRAN package, but it depends on Bioconductor packages, so we put ;; it here. (define-public r-activedriverwgs