From unknown Sun Jun 22 04:06:35 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#58806] [PATCH] gnu: Add r-baalchip. Resent-From: =?UTF-8?Q?M=C4=83d=C4=83lin?= Ionel =?UTF-8?Q?Patra=C8=99cu?= Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Wed, 26 Oct 2022 22:39:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 58806 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 58806@debbugs.gnu.org X-Debbugs-Original-To: Received: via spool by submit@debbugs.gnu.org id=B.16668239288960 (code B ref -1); Wed, 26 Oct 2022 22:39:01 +0000 Received: (at submit) by debbugs.gnu.org; 26 Oct 2022 22:38:48 +0000 Received: from localhost ([127.0.0.1]:55469 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1onp2t-0002KR-PB for submit@debbugs.gnu.org; Wed, 26 Oct 2022 18:38:48 -0400 Received: from lists.gnu.org ([209.51.188.17]:54426) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1onp2p-0002KF-2w for submit@debbugs.gnu.org; Wed, 26 Oct 2022 18:38:46 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1onp2o-0001uf-Th for guix-patches@gnu.org; Wed, 26 Oct 2022 18:38:42 -0400 Received: from a2062.mx.srv.dfn.de ([194.95.232.172]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1onp2m-0007OW-Ly for guix-patches@gnu.org; Wed, 26 Oct 2022 18:38:42 -0400 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; s=mdc; t=1666823901; x=1668638302; bh=x08MZw4tV7lG5em 4RQMVzgmhfgS9XP+JgIgWOx0oAFU=; b=i4TsDcyiK3zIzK0BE5vG69mtvaFa9SZ A9LXnDbub5++vT0TNTLSf8SMLNmKzVWmfEloMKkwqyQBCdgSMZAYkWp+px87rQMB 2x/qRFh59UkkNjMjsbXjarm04/jA58O0J3COiaHxxDknJ1vaP2jTLWZAtD/fM/YG xoQPrrADDcbo= 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 id 4907BA025C for ; Thu, 27 Oct 2022 00:38:20 +0200 (CEST) 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 15.1.2507.13; Thu, 27 Oct 2022 00:38:20 +0200 From: =?UTF-8?Q?M=C4=83d=C4=83lin?= Ionel =?UTF-8?Q?Patra=C8=99cu?= Date: Thu, 27 Oct 2022 00:38:09 +0200 Message-ID: <20221026223809.29865-1-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.37.3 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-14.0.0.3092-9.0.1002-27226.003 X-TM-AS-Result: No-10--0.554000-5.000000 X-TMASE-MatchedRID: kREspPIIG7SaVzGETDUtnArcxrzwsv5uwTlc9CcHMZerwqxtE531VIPc XuILVCbaRRa406V/YwyBUGewL2YXt7BgXed5LSW6qhcdnP91eXHF0kjYVlocoeKYpwtG+wHVTHK WCmR2jKWKbindmE5bmMCrMSR+lfKoiCsqewnUZGAGTYh4hC/PnzibQmxbrchcZOeUz4oLoaVvQa rAmyn3EW/Sm1UTYSjFR0dsVbq5fRkUegcXwBHh+8Yv//yaWh0Dbv9wX5p41kyUKS3slq009Z4CI KY/Hg3AGdQnQSTrKGPEQdG7H66TyN+E/XGDLHcMQiEHN8fAQeFXGprG9PtVHdPkX8E5/LzlM9/3 EnEl9BTppsY9fFkexKf4VMPRm0DrjPEajiOo/57FccpR0R4r1s52AwaqKJKD3FJHtt7t+dMVOzi WO23T3g/Yr/7CTLFXOzsov7pcUHilIGXSGl4OHw== X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--0.554000-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27226.003 X-TM-SNTS-SMTP: 475AB680A97F5699D1DB6F77E345C6F0E84317CD1A59EA8375769704D5AFC1E52002: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-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 (--) X-Debbugs-Cc: rekado@elephly.net * gnu/packages/bioconductor.scm (r-baalchip): New variable. --- gnu/packages/bioconductor.scm | 45 +++++++++++++++++++++++++++++++++++ 1 file changed, 45 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 3692bb94af..23991983da 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2293,6 +2293,51 @@ (define-public r-antiprofiles tumor samples from healthy controls.") (license license:artistic2.0))) +(define-public r-baalchip + (package + (name "r-baalchip") + (version "1.22.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "BaalChIP" version)) + (sha256 + (base32 + "02qwk9n2fyg5f9xxjiiha9mi6p9ii3zi5x7w84sh5d5g58s27g6q")))) + (properties `((upstream-name . "BaalChIP"))) + (build-system r-build-system) + (arguments + '(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'set-HOME + (lambda _ (setenv "HOME" "/tmp")))))) + (inputs (list perl)) ;; extra/get.overlaps.v2_chrXY.perl + (propagated-inputs + (list r-coda + r-doby + r-doparallel + r-foreach + r-genomeinfodb + r-genomicalignments + r-genomicranges + r-ggplot2 + r-iranges + r-reshape2 + r-rsamtools + r-scales)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/BaalChIP") + (synopsis + "Analysis of allele-specific transcription factor binding in cancer genomes") + (description + "The package offers functions to process multiple @code{ChIP-seq BAM} files +and detect allele-specific events. Computes allele counts at individual variants +(SNPs/SNVs), implements extensive @dfn{QC} (quality control) steps to remove +problematic variants, and utilizes a Bayesian framework to identify statistically +significant allele-specific events. @code{BaalChIP} is able to account for copy +number differences between the two alleles, a known phenotypical feature of cancer +samples.") + (license license:artistic2.0))) + (define-public r-biocversion (package (name "r-biocversion") base-commit: a2e4e3489b4fdec6e270c93fcd9724abe983217e -- 2.37.3 From unknown Sun Jun 22 04:06:35 2025 MIME-Version: 1.0 X-Mailer: MIME-tools 5.505 (Entity 5.505) X-Loop: help-debbugs@gnu.org From: help-debbugs@gnu.org (GNU bug Tracking System) To: =?UTF-8?Q?M=C4=83d=C4=83lin?= Ionel =?UTF-8?Q?Patra=C8=99cu?= Subject: bug#58806: closed ([PATCH] gnu: Add r-baalchip.) Message-ID: References: <87o7txiiqj.fsf@elephly.net> <20221026223809.29865-1-madalinionel.patrascu@mdc-berlin.de> X-Gnu-PR-Message: they-closed 58806 X-Gnu-PR-Package: guix-patches X-Gnu-PR-Keywords: patch Reply-To: 58806@debbugs.gnu.org Date: Thu, 27 Oct 2022 11:56:02 +0000 Content-Type: multipart/mixed; boundary="----------=_1666871762-1167-1" This is a multi-part message in MIME format... ------------=_1666871762-1167-1 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="utf-8" Your bug report #58806: [PATCH] gnu: Add r-baalchip. which was filed against the guix-patches package, has been closed. The explanation is attached below, along with your original report. If you require more details, please reply to 58806@debbugs.gnu.org. --=20 58806: https://debbugs.gnu.org/cgi/bugreport.cgi?bug=3D58806 GNU Bug Tracking System Contact help-debbugs@gnu.org with problems ------------=_1666871762-1167-1 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at 58806-done) by debbugs.gnu.org; 27 Oct 2022 11:55:29 +0000 Received: from localhost ([127.0.0.1]:56340 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1oo1Tt-0000I1-Gw for submit@debbugs.gnu.org; Thu, 27 Oct 2022 07:55:29 -0400 Received: from sender4-of-o51.zoho.com ([136.143.188.51]:21132) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1oo1Tn-0000Hp-Uw for 58806-done@debbugs.gnu.org; Thu, 27 Oct 2022 07:55:27 -0400 ARC-Seal: i=1; a=rsa-sha256; t=1666871721; cv=none; d=zohomail.com; s=zohoarc; b=QPnjVRrqcZZDRzXJpxebL2nYcaziKW38NRf7E4h0AH5s2hC147G8KuEMlIj1E6g6+DPwNp3wt3tf6Cc99s1w0n0Kc5EK0jGMEi+bDHZSyBHW4Yg3ZMkU88Zw2opYrouVEAMH9jQeUJuXs6vX6xlLrAeuU2RRfcnOR7bCHBdpBKc= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1666871721; h=Content-Type:Date:From:MIME-Version:Message-ID:Subject:To; bh=6MRBgA9hFv8LM+wOeuHRT38czJCMGVRlNPoUAXLAXbE=; b=GKKu5IjQ9VSPq1M5o5ThT/wj94CV+dvA/BkJhgPmi3L9ZHW4UlVMXN/jDqX9xDMaOIM+cmBBpAR3LrvU9CiDLXxvZJBypP5E3NPTXD7mdcUat1pVPQRYOKF+XKHMg7tqrNRTXyjkfcytQsgDp0IC4fsUTF/ZvHmHOvFacf9dfwg= 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=1666871721; s=zoho; d=elephly.net; i=rekado@elephly.net; h=From:From:To:To:Subject:Subject:Date:Date:Message-ID:MIME-Version:Content-Type:Message-Id:Reply-To:Cc; bh=6MRBgA9hFv8LM+wOeuHRT38czJCMGVRlNPoUAXLAXbE=; b=IXp3BI2FjjPArorJPo0YMlNSAHOe5leuivJQxpgS50fK4iAfBU2aN3onXNR0OGfq w9F+fMuNS+7OwX+gEWAUw74/WSy8UNPc99r+xMTD8+MUgxtWpc8ztnbL56oe8sO3LdX h2Rd3oSAZZmoTYmGXv/MimjLgNQx7qRRtOTKa+Bc= Received: from localhost (151-110-142-46.pool.kielnet.net [46.142.110.151]) by mx.zohomail.com with SMTPS id 166687171894018.90177457448783; Thu, 27 Oct 2022 04:55:18 -0700 (PDT) User-agent: mu4e 1.8.9; emacs 28.1 From: Ricardo Wurmus To: 58806-done@debbugs.gnu.org Subject: [PATCH] gnu: Add r-baalchip. Date: Thu, 27 Oct 2022 13:55:00 +0200 X-URL: https://elephly.net X-PGP-Key: https://elephly.net/rekado.pubkey X-PGP-Fingerprint: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC Message-ID: <87o7txiiqj.fsf@elephly.net> MIME-Version: 1.0 Content-Type: text/plain X-ZohoMailClient: External X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 58806-done 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: -1.0 (-) Applied with minor changes. Thanks! -- Ricardo ------------=_1666871762-1167-1 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at submit) by debbugs.gnu.org; 26 Oct 2022 22:38:48 +0000 Received: from localhost ([127.0.0.1]:55469 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1onp2t-0002KR-PB for submit@debbugs.gnu.org; Wed, 26 Oct 2022 18:38:48 -0400 Received: from lists.gnu.org ([209.51.188.17]:54426) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1onp2p-0002KF-2w for submit@debbugs.gnu.org; Wed, 26 Oct 2022 18:38:46 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1onp2o-0001uf-Th for guix-patches@gnu.org; Wed, 26 Oct 2022 18:38:42 -0400 Received: from a2062.mx.srv.dfn.de ([194.95.232.172]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1onp2m-0007OW-Ly for guix-patches@gnu.org; Wed, 26 Oct 2022 18:38:42 -0400 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; s=mdc; t=1666823901; x=1668638302; bh=x08MZw4tV7lG5em 4RQMVzgmhfgS9XP+JgIgWOx0oAFU=; b=i4TsDcyiK3zIzK0BE5vG69mtvaFa9SZ A9LXnDbub5++vT0TNTLSf8SMLNmKzVWmfEloMKkwqyQBCdgSMZAYkWp+px87rQMB 2x/qRFh59UkkNjMjsbXjarm04/jA58O0J3COiaHxxDknJ1vaP2jTLWZAtD/fM/YG xoQPrrADDcbo= 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 id 4907BA025C for ; Thu, 27 Oct 2022 00:38:20 +0200 (CEST) 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 15.1.2507.13; Thu, 27 Oct 2022 00:38:20 +0200 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= To: Subject: [PATCH] gnu: Add r-baalchip. Date: Thu, 27 Oct 2022 00:38:09 +0200 Message-ID: <20221026223809.29865-1-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.37.3 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-14.0.0.3092-9.0.1002-27226.003 X-TM-AS-Result: No-10--0.554000-5.000000 X-TMASE-MatchedRID: kREspPIIG7SaVzGETDUtnArcxrzwsv5uwTlc9CcHMZerwqxtE531VIPc XuILVCbaRRa406V/YwyBUGewL2YXt7BgXed5LSW6qhcdnP91eXHF0kjYVlocoeKYpwtG+wHVTHK WCmR2jKWKbindmE5bmMCrMSR+lfKoiCsqewnUZGAGTYh4hC/PnzibQmxbrchcZOeUz4oLoaVvQa rAmyn3EW/Sm1UTYSjFR0dsVbq5fRkUegcXwBHh+8Yv//yaWh0Dbv9wX5p41kyUKS3slq009Z4CI KY/Hg3AGdQnQSTrKGPEQdG7H66TyN+E/XGDLHcMQiEHN8fAQeFXGprG9PtVHdPkX8E5/LzlM9/3 EnEl9BTppsY9fFkexKf4VMPRm0DrjPEajiOo/57FccpR0R4r1s52AwaqKJKD3FJHtt7t+dMVOzi WO23T3g/Yr/7CTLFXOzsov7pcUHilIGXSGl4OHw== X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--0.554000-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27226.003 X-TM-SNTS-SMTP: 475AB680A97F5699D1DB6F77E345C6F0E84317CD1A59EA8375769704D5AFC1E52002: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 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 (--) X-Debbugs-Cc: rekado@elephly.net * gnu/packages/bioconductor.scm (r-baalchip): New variable. --- gnu/packages/bioconductor.scm | 45 +++++++++++++++++++++++++++++++++++ 1 file changed, 45 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 3692bb94af..23991983da 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2293,6 +2293,51 @@ (define-public r-antiprofiles tumor samples from healthy controls.") (license license:artistic2.0))) +(define-public r-baalchip + (package + (name "r-baalchip") + (version "1.22.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "BaalChIP" version)) + (sha256 + (base32 + "02qwk9n2fyg5f9xxjiiha9mi6p9ii3zi5x7w84sh5d5g58s27g6q")))) + (properties `((upstream-name . "BaalChIP"))) + (build-system r-build-system) + (arguments + '(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'set-HOME + (lambda _ (setenv "HOME" "/tmp")))))) + (inputs (list perl)) ;; extra/get.overlaps.v2_chrXY.perl + (propagated-inputs + (list r-coda + r-doby + r-doparallel + r-foreach + r-genomeinfodb + r-genomicalignments + r-genomicranges + r-ggplot2 + r-iranges + r-reshape2 + r-rsamtools + r-scales)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/BaalChIP") + (synopsis + "Analysis of allele-specific transcription factor binding in cancer genomes") + (description + "The package offers functions to process multiple @code{ChIP-seq BAM} files +and detect allele-specific events. Computes allele counts at individual variants +(SNPs/SNVs), implements extensive @dfn{QC} (quality control) steps to remove +problematic variants, and utilizes a Bayesian framework to identify statistically +significant allele-specific events. @code{BaalChIP} is able to account for copy +number differences between the two alleles, a known phenotypical feature of cancer +samples.") + (license license:artistic2.0))) + (define-public r-biocversion (package (name "r-biocversion") base-commit: a2e4e3489b4fdec6e270c93fcd9724abe983217e -- 2.37.3 ------------=_1666871762-1167-1--