From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from mp10.migadu.com ([2001:41d0:8:6d80::]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits)) by ms5.migadu.com with LMTPS id 6AlYBtQjumKDfwEAbAwnHQ (envelope-from ) for ; Mon, 27 Jun 2022 23:40:36 +0200 Received: from aspmx1.migadu.com ([2001:41d0:8:6d80::]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits)) by mp10.migadu.com with LMTPS id sHdpBdQjumKPEAEAG6o9tA (envelope-from ) for ; Mon, 27 Jun 2022 23:40:36 +0200 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (No client certificate requested) by aspmx1.migadu.com (Postfix) with ESMTPS id B784F1A99A for ; Mon, 27 Jun 2022 23:40:35 +0200 (CEST) Received: from localhost ([::1]:40678 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1o5wTC-0006Kt-7l for larch@yhetil.org; Mon, 27 Jun 2022 17:40:34 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:34088) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1o5wSh-0006Jq-5P for guix-patches@gnu.org; Mon, 27 Jun 2022 17:40:04 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:59606) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1o5wSg-0007GM-31 for guix-patches@gnu.org; Mon, 27 Jun 2022 17:40:02 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1o5wSg-0007Ko-0i for guix-patches@gnu.org; Mon, 27 Jun 2022 17:40:02 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#56267] [PATCH] gnu: Add r-badregionfinder. 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: Mon, 27 Jun 2022 21:40:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 56267 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 56267@debbugs.gnu.org X-Debbugs-Original-To: Received: via spool by submit@debbugs.gnu.org id=B.165636599828179 (code B ref -1); Mon, 27 Jun 2022 21:40:01 +0000 Received: (at submit) by debbugs.gnu.org; 27 Jun 2022 21:39:58 +0000 Received: from localhost ([127.0.0.1]:53503 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1o5wSc-0007KR-ET for submit@debbugs.gnu.org; Mon, 27 Jun 2022 17:39:58 -0400 Received: from lists.gnu.org ([209.51.188.17]:48080) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1o5wSa-0007KI-Fl for submit@debbugs.gnu.org; Mon, 27 Jun 2022 17:39:56 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:34080) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1o5wSZ-0006Ef-T5 for guix-patches@gnu.org; Mon, 27 Jun 2022 17:39:56 -0400 Received: from b2062.mx.srv.dfn.de ([194.95.234.172]:40335) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1o5wSW-0007EO-8t for guix-patches@gnu.org; Mon, 27 Jun 2022 17:39:55 -0400 Received: from localhost (localhost [127.0.0.1]) by b2062.mx.srv.dfn.de (Postfix) with ESMTP id E77BB160253 for ; Mon, 27 Jun 2022 23:39:47 +0200 (CEST) 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=1656365987; x=1658180388; bh=1nhOQjhDf5pB0lM6cYbY4oAWB2MLFOvs4BFZQer8Wac=; b=WOjhZ1vxAgm/ D7CrGJHu7HD9uclHil08u4GX2K4Q/y6guecHfQUALoI+MhfsGITGcEwZK+j7Uttg Oa9LScQMDIHkk8lYHR28FWzShT6qU8hVjjshp4VGqKoHDVS4+yZ+5H5nQyf+KN81 3cvAQiP2fFbriWzmDFGixUU2M5YHBhA= 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 BrJLtiawQXXB for ; Mon, 27 Jun 2022 23:39:47 +0200 (CEST) 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 for ; Mon, 27 Jun 2022 23:39:47 +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 15.1.2507.9; Mon, 27 Jun 2022 23:39:46 +0200 From: =?UTF-8?Q?M=C4=83d=C4=83lin?= Ionel =?UTF-8?Q?Patra=C8=99cu?= Date: Mon, 27 Jun 2022 23:39:36 +0200 Message-ID: <20220627213936.19198-1-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.36.1 MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Content-Type: text/plain X-Originating-IP: [141.80.113.106] X-ClientProxiedBy: SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-26982.003 X-TM-AS-Result: No-10--3.687900-5.000000 X-TMASE-MatchedRID: /+von0vPuFH/R1NSMc2qCU7nLUqYrlslFIuBIWrdOeOjEIt+uIPPOAbo TDS3zulAcjTcMkuJPYkZijt1cgK90C/33TWoSUH6194/5X9VfCxReWnUUdhI9ToUdFbHYUawycO hvTXTlouSkIUZyUQUJxJTjjs9yT6Yo8WMkQWv6iXBcIE78YqRWvcUt5lc1lLgNedi3nDhxyOAdc X2zDkOejHdo5xzO+a4beBGtY+ov2aZtPk4ghGYjq1QWHsbfROT58l+vjTR3SipK53CsSzX7H/xQ 83+QIMxgOXN5nbVKsaZAdYQCzgVcdm2xSyikSK/tOdWe/Uk/vuwZO9kmaWWvP8+E8vSQCkfySOb 56URxsg= X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--3.687900-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-26982.003 X-TM-SNTS-SMTP: ACA1B6554465B7D34F5953850C50B748F6920B0D1020FC830C85954ED2CB33792002:F Received-SPF: pass client-ip=194.95.234.172; envelope-from=MadalinIonel.Patrascu@mdc-berlin.de; helo=b2062.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, T_SCC_BODY_TEXT_LINE=-0.01 autolearn=ham autolearn_force=no X-Spam_action: no action 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+larch=yhetil.org@gnu.org Sender: "Guix-patches" X-Migadu-Flow: FLOW_IN X-Migadu-To: larch@yhetil.org X-Migadu-Country: US ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=yhetil.org; s=key1; t=1656366035; h=from:from:sender:sender:reply-to:subject:subject:date:date: message-id:message-id:to:to:cc:mime-version:mime-version: content-type:content-type: content-transfer-encoding:content-transfer-encoding:resent-cc: resent-from:resent-sender:resent-message-id:list-id:list-help: list-unsubscribe:list-subscribe:list-post:dkim-signature; bh=3hY4WYX7JQSdbvMM3s4zkGz31Ej3LkVHKvr+L0Dm2PA=; b=qhKGzjfEt0InVEAE4qWl434soPwS1RqtA6x+Pltjp09znjQmXX5hSHK9+7ZCYZYpENm1ic zCoKBHWQ7Izh0gNlbFmNBKAQVQmBJUflyXL2XjZ+n4jXWszTs1aD5fn7Eri5hx7MklS2Kw 8yCwuQT7y3ObisSgBGYpX0JKYamqxv2qKw3xeZE3yxPFMs88SwR8iYWHjKSWzCHZuXQXQo Fg2Uyn5+e6ZPiSBonrQFMhWisj4lAKYDBEvlswLeicBDP+VkRkQfKMWrrEEZVhrCMPZ0bX fVRIlD9V3bD0v95uoS+FRtyTEeM5RwUy4aKJTOG2k4qe9H7lTKjo5F6VvL6PBg== ARC-Seal: i=1; s=key1; d=yhetil.org; t=1656366035; a=rsa-sha256; cv=none; b=qGvXskxm3oRHnL75HAXyBWp8gxwVvhSxMIReGR5R+CJBl6oC+8IbuEKhqPOnxqYV8YHJdm xCq2ZV04BgGrVVQ9amEPRe3pRYCDjrJwLf/iXZJnJsgM1C88OdsgTNLTQR5ZHglPtRDUtc 1T+YzConsKdg6tX34vSItTVIRankNflrm1zk3n/Mvy0Wsk0Y037hp/BInT5uVM/G99fzu4 MR59PZrtQSk0klAw+QxY6vGGAGwuyljPKdRqw5o3uuA2eBLHD6y+ZDDGnWHG7WeQZqQQl+ HvZBD34Cb8+i4y7EJmMQxn0DrxrRkhw7iSdPME4GwsCOQPNh4HLygd1U3BcBQA== ARC-Authentication-Results: i=1; aspmx1.migadu.com; dkim=fail ("headers rsa verify failed") header.d=mdc-berlin.de header.s=mdc header.b=WOjhZ1vx; dmarc=fail reason="SPF not aligned (relaxed)" header.from=mdc-berlin.de (policy=none); spf=pass (aspmx1.migadu.com: domain of "guix-patches-bounces+larch=yhetil.org@gnu.org" designates 209.51.188.17 as permitted sender) smtp.mailfrom="guix-patches-bounces+larch=yhetil.org@gnu.org" X-Migadu-Spam-Score: 6.45 Authentication-Results: aspmx1.migadu.com; dkim=fail ("headers rsa verify failed") header.d=mdc-berlin.de header.s=mdc header.b=WOjhZ1vx; dmarc=fail reason="SPF not aligned (relaxed)" header.from=mdc-berlin.de (policy=none); spf=pass (aspmx1.migadu.com: domain of "guix-patches-bounces+larch=yhetil.org@gnu.org" designates 209.51.188.17 as permitted sender) smtp.mailfrom="guix-patches-bounces+larch=yhetil.org@gnu.org" X-Migadu-Queue-Id: B784F1A99A X-Spam-Score: 6.45 X-Migadu-Scanner: scn0.migadu.com X-TUID: U+jvDLwXvKFT * gnu/packages/bioconductor.scm (r-badregionfinder): 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 1e87b190c2..aa4ba4706d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2029,6 +2029,34 @@ (define-public r-aneufinder sequencing data.") (license license:artistic2.0))) +(define-public r-badregionfinder + (package + (name "r-badregionfinder") + (version "1.24.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "BadRegionFinder" version)) + (sha256 + (base32 + "1a1pqmh5ak9s3k1lxw6flanchk24zyznwm34ixi2b78wdc3hqgm9")))) + (properties `((upstream-name . "BadRegionFinder"))) + (build-system r-build-system) + (propagated-inputs + (list r-biomart + r-genomicranges + r-rsamtools + r-s4vectors + r-variantannotation)) + (home-page "https://bioconductor.org/packages/BadRegionFinder") + (synopsis "Identifying regions with bad coverage in sequence alignment data") + (description + "@code{BadRegionFinder} is a package for identifying regions with a bad, +acceptable and good coverage in sequence alignment data available as bam files. +The whole genome may be considered as well as a set of target regions. Various +visual and textual types of output are available.") + (license license:lgpl3))) + + (define-public r-biocversion (package (name "r-biocversion") base-commit: 144a750f8b10e606751bc887bcb09e7fb7ae09ff -- 2.36.1