From debbugs-submit-bounces@debbugs.gnu.org Mon Dec 13 06:52:43 2021 Received: (at submit) by debbugs.gnu.org; 13 Dec 2021 11:52:43 +0000 Received: from localhost ([127.0.0.1]:54274 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1mwjsp-0005Zk-Do for submit@debbugs.gnu.org; Mon, 13 Dec 2021 06:52:43 -0500 Received: from lists.gnu.org ([209.51.188.17]:35348) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1mwjsl-0005ZZ-0J for submit@debbugs.gnu.org; Mon, 13 Dec 2021 06:52:42 -0500 Received: from eggs.gnu.org ([209.51.188.92]:54906) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1mwjsk-0005ys-HA for guix-patches@gnu.org; Mon, 13 Dec 2021 06:52:38 -0500 Received: from a2062.mx.srv.dfn.de ([194.95.232.172]:56561) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1mwjsh-00051N-9q for guix-patches@gnu.org; Mon, 13 Dec 2021 06:52:37 -0500 Received: from localhost (localhost [127.0.0.1]) by a2062.mx.srv.dfn.de (Postfix) with ESMTP id 614A7A02FB for ; Mon, 13 Dec 2021 12:52:18 +0100 (CET) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-type:content-type:content-transfer-encoding:mime-version :x-mailer:message-id:date:date:subject:subject:from:from :received:received:received; s=mdc; t=1639396337; x=1641210738; bh=RUkQnlUnvcYRUlQKhttctFIQWsuG4oTOUYW6Skv0RKw=; b=Cv1MeAdK3lzD YGTPlS7DPdP+hJK8xO2hw/l0ypCuxIInXBo9WkMpruFViy/vre+NedfT0nHRszvD UKVny1U0C+iO+Hq1e+mJw9848md18cfs1oKzlCs8dp1ti0ECKt+N6gcjgNacLCa5 qk5Ef2dQX5QeZqqXXlDu2gSvwyKAMm0= Received: from a2062.mx.srv.dfn.de ([127.0.0.1]) by localhost (mgw4-han.srv.dfn.de [127.0.0.1]) (amavisd-new, port 20134) with ESMTP id jwqfE-NsLP4O for ; Mon, 13 Dec 2021 12:52:17 +0100 (CET) Received: from SW-IT-P-EX4.mdc-berlin.net (mgw4.mdc-berlin.de [141.80.113.62]) by a2062.mx.srv.dfn.de (Postfix) with ESMTPS for ; Mon, 13 Dec 2021 12:52:17 +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 15.1.2375.17; Mon, 13 Dec 2021 12:52:17 +0100 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= To: Subject: [PATCH] gnu: Add r-chromvarmotifs. Date: Mon, 13 Dec 2021 12:52:07 +0100 Message-ID: <20211213115207.14186-1-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.34.0 MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Content-Type: text/plain 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-14.0.0.3092-8.6.1018-26586.007 X-TM-AS-Result: No-10-0.070200-8.000000 X-TMASE-MatchedRID: 2mVTIgh7BvFlaC2eEN9gWz8Ckw9b/GFeVBDQSDMig9F0HeSw1vKRpTwD GrXuzHSkRRa406V/YwwKl5/g/W44hoeo25/FaNFLrKAvSPiudyH4qCLIu0mtIGmyCG+JylaLCe8 AXH4vSUSaoEAdxdGfWa8DjUKIOK5YtSNQjXFRF07dCok3ibXlQeuLFZZYlisfHxPMjOKY7A8Lbi gRnpKlKTpcQTtiHDgWukBBVdVRO05QMgHdCOx1k6jHqWlKaQVNAegxjTNvuBQt/AVDgPUsXFwjs Iw4QUxg5RvpxvQFt2q6jXhOVjEofIVVN2jRuEqVt0oQIuj+SVeFEVfQxs3N6ZDgmt8QekvB5maC eNv/LIyDbTfm4VqakJRMZUCEHkRt X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10-0.070200-8.000000 X-TMASE-Version: SMEX-14.0.0.3092-8.6.1018-26586.007 X-TM-SNTS-SMTP: 7BCBDBF0917C7FE18596C039ACE2FC9D4D6B0429CB35E1A553C489BDC8684D2C2000:F Received-SPF: pass client-ip=194.95.232.172; envelope-from=MadalinIonel.Patrascu@mdc-berlin.de; helo=a2062.mx.srv.dfn.de X-Spam_score_int: -43 X-Spam_score: -4.4 X-Spam_bar: ---- X-Spam_report: (-4.4 / 5.0 requ) BAYES_00=-1.9, DKIM_SIGNED=0.1, DKIM_VALID=-0.1, DKIM_VALID_AU=-0.1, DKIM_VALID_EF=-0.1, RCVD_IN_DNSWL_MED=-2.3, SPF_HELO_PASS=-0.001, SPF_PASS=-0.001 autolearn=ham autolearn_force=no X-Spam_action: no action X-Spam-Score: -1.4 (-) X-Debbugs-Envelope-To: submit Cc: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -2.4 (--) * gnu/packages/bioconductor.scm (r-chromvarmotifs): New variable. This package is not a bioconductor one, but it use the r-tfbstools that is stored in bioconductor.scm. If I used the cran.scm for the current definition I should import the bioconductor and it already imports cran. Beside this the package is somehow related with other bioconductor packages. --- gnu/packages/bioconductor.scm | 29 +++++++++++++++++++++++++++++ 1 file changed, 29 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 44bf5c7d24..28cc8b7458 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1183,6 +1183,35 @@ (define-public r-chromstardata chromstaR package.") (license license:gpl3))) +(define-public r-chromvarmotifs + (let + ((commit "38bed559c1f4770b6c91c80bf3f8ea965da26076") + (revision "1")) + (package + (name "r-chromvarmotifs") + (version (git-version "0.2.0" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/GreenleafLab/chromVARmotifs") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0i9v1m1hrg1lkd2pnkj5nnrpks6vhhhpbdhsfl2lmjak4npxxr5q")))) + (properties `((upstream-name . "chromVARmotifs"))) + (build-system r-build-system) + (propagated-inputs + `(("r-tfbstools" ,r-tfbstools))) + (home-page "https://github.com/GreenleafLab/chromVARmotifs") + (synopsis "Stores motif collections for use with motifmatchr or chromVAR") + (description + "This package @code{r-chromvarmotifs} stores motifs collections as +lists of @dfn{position frequency matrix} (PWMatrixList) objects provided by +@code{TFBSTools} package for use in R with packages like @code{motifmatchr} or +@code{chromVAR}.") + (license license:expat)))) + (define-public r-copyhelper (package (name "r-copyhelper") -- 2.34.0 From debbugs-submit-bounces@debbugs.gnu.org Mon Dec 13 07:39:39 2021 Received: (at 52463-done) by debbugs.gnu.org; 13 Dec 2021 12:39:39 +0000 Received: from localhost ([127.0.0.1]:54329 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1mwkcF-0000XU-3H for submit@debbugs.gnu.org; Mon, 13 Dec 2021 07:39:39 -0500 Received: from sender3-of-o51.zoho.com ([136.143.184.51]:21745) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1mwkcD-0000XK-2I for 52463-done@debbugs.gnu.org; Mon, 13 Dec 2021 07:39:38 -0500 ARC-Seal: i=1; a=rsa-sha256; t=1639399172; cv=none; d=zohomail.com; s=zohoarc; b=aH5BjaFrlZlyloVUlxXkXeVylwyJvf9a+RJErRkMGZ3C3BxNgLzhN0SSExQGfJXt0rJSydlHtWX9fGcUeraAf7ka8+zPRRo1kwfyrmgFNXeqPjL8Kw7CqhItstOwJ2eISGsb2Xd5KtkySVfOg3Tngx8CsQZRVIhS2vNlGlVMPsg= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1639399172; h=Content-Type:Content-Transfer-Encoding:Cc:Date:From:MIME-Version:Message-ID:Subject:To; bh=zSrCt9Tem20Sui9ExJKoz/O17uSzCbCKeOS0CxTOI4o=; b=enlFmMW9DspXOxZoNNv3FwfFcTAM4DxBsDFLiMLpS5jDoiTmZbKlgjW1eDFT6bSWZnp+zlpm7P00G6WaQVE0j0OVBieTxDH0FrqZC0mI5X1eBIndnZbizfLkgtS02xmKydru/XqUFwQsqpj32uVX64nP8rzzuUFNX3vH19bCMZo= ARC-Authentication-Results: i=1; mx.zohomail.com; dkim=pass header.i=elephly.net; spf=pass smtp.mailfrom=rekado@elephly.net; dmarc=pass header.from= DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; t=1639399172; s=zoho; d=elephly.net; i=rekado@elephly.net; h=From:To:Cc:Subject:Date:Message-ID:MIME-Version:Content-Type:Content-Transfer-Encoding; bh=zSrCt9Tem20Sui9ExJKoz/O17uSzCbCKeOS0CxTOI4o=; b=CH1q6z5ku19B8b8tdxwg6NxaqgNa0YOYkT96yP5mM8rbIEFilf8WyYbwX9h+pN7n 40wYJaG9lDVEvqtnbyu0LXC2I6Tw7h7N7IuWsf7eXBVWmIdDT+c/N4v3KMuLW4IJ65r sKVdZVE/+l67dSNqr7iBfhOeuYn5c42puzxxomII= Received: from localhost (p54ad4933.dip0.t-ipconnect.de [84.173.73.51]) by mx.zohomail.com with SMTPS id 1639399171913544.69928232104; Mon, 13 Dec 2021 04:39:31 -0800 (PST) User-agent: mu4e 1.6.6; emacs 28.0.50 From: Ricardo Wurmus To: 52463-done@debbugs.gnu.org Subject: [PATCH] gnu: Add r-chromvarmotifs. 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