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Resent-From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Original-Sender: "Debbugs-submit" Resent-CC: rekado@elephly.net, guix-patches@gnu.org Resent-Date: Mon, 20 Mar 2023 16:01:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 62297 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: <62297@debbugs.gnu.org> Cc: rekado@elephly.net X-Debbugs-Original-Xcc: rekado@elephly.net Received: via spool by 62297-submit@debbugs.gnu.org id=B62297.16793280284439 (code B ref 62297); Mon, 20 Mar 2023 16:01:02 +0000 Received: (at 62297) by debbugs.gnu.org; 20 Mar 2023 16:00:28 +0000 Received: from localhost ([127.0.0.1]:55544 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1peHvw-00019R-1H for submit@debbugs.gnu.org; Mon, 20 Mar 2023 12:00:28 -0400 Received: from a2062.mx.srv.dfn.de ([194.95.232.172]:52479) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1peHvt-00018r-UA for 62297@debbugs.gnu.org; Mon, 20 Mar 2023 12:00:26 -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 :references:in-reply-to:x-mailer:message-id:date:date:subject :subject:from:from:received; s=mdc; t=1679328019; x=1681142420; bh=jH63PiQiMbHypCdwhMTxd6j7SbjviaIPW/hK8XBj/wg=; b=gGIP9FrhQd9n rI16czFgM3nfNHfeoaiJSGgrD38x57WNsCaMoVxu9B6PvQw8+cr0+p3TQK5BFhix dYNzoja61SAtnI2k1oZljL4lFd1X7pGg0YRIdQsUbaLm3cP3WMeEIv/jnnaDcr0I n3/ydVYCn/IOgXS4WW57lw6raHzE/nE= 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 CC0E7A014A for <62297@debbugs.gnu.org>; Mon, 20 Mar 2023 17:00:19 +0100 (CET) Received: from pimi-TRX40-AORUS-PRO-WIFI.lan (77.23.232.54) 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 15.1.2507.21; Mon, 20 Mar 2023 17:00:18 +0100 From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Date: Mon, 20 Mar 2023 17:00:05 +0100 Message-ID: <20230320160005.1594550-5-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.39.2 In-Reply-To: <20230320160005.1594550-1-madalinionel.patrascu@mdc-berlin.de> References: <20230320160005.1594550-1-madalinionel.patrascu@mdc-berlin.de> MIME-Version: 1.0 X-Originating-IP: [77.23.232.54] 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-14.0.0.3092-9.0.1002-27516.000 X-TM-AS-Result: No-10--5.484200-5.000000 X-TMASE-MatchedRID: 2wfub8HDRfP/R1NSMc2qCU7nLUqYrlslFIuBIWrdOePfUZT83lbkEENK xNfKw7SiRRa406V/YwyBUGewL2YXt0fr6WG4Th9aDDzmS9l9fYoXivwflisSrNWM2x6EZ/S97Sc dpy2ZKwJOM4h+YsvDLlPSAWHDBcnd/2fkqsLULy4APmNKDWsW0JobBmSkKst1Ipz++XQI8PGeAi CmPx4NwBnUJ0Ek6yhjxEHRux+uk8hfNjF5BHUO+xAP38E9e8ZMtOETm+G1DiFM4bjy4WN0/32dn ZE+UfYT0Fw07uQGltQ= X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--5.484200-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27516.000 X-TM-SNTS-SMTP: 26A051E8CFB21774DDF2DAFDF62FEB4F9FC038B5B427FE58796C2BA0F67371732002: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-bounces+patchwork=mira.cbaines.net@gnu.org X-getmail-retrieved-from-mailbox: Patches * gnu/packages/bioconductor.scm (r-annotationhubdata): New variable. --- gnu/packages/bioconductor.scm | 53 +++++++++++++++++++++++++++++++++++ 1 file changed, 53 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 78ce740c2c..8ebdcc3706 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2704,6 +2704,59 @@ (define-public r-animalcules to understand their data better and discover new insights.") (license license:artistic2.0))) +(define-public r-annotationhubdata + (package + (name "r-annotationhubdata") + (version "1.28.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "AnnotationHubData" version)) + (sha256 + (base32 "0mcx09kcxccw2gkf4c3w7sxgb7v3gwbvahvx9wgq8f93q85yzg95")))) + (properties `((upstream-name . "AnnotationHubData"))) + (build-system r-build-system) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + (add-before 'install 'change-home-dir + (lambda _ + ;; Change from /homeless-shelter to /tmp for write permission. + (setenv "HOME" "/tmp")))))) + (propagated-inputs + (list r-annotationdbi + r-annotationforge + r-annotationhub + r-biobase + r-bioccheck + r-biocgenerics + r-biocmanager + r-biocviews + r-biostrings + r-dbi + r-futile-logger + r-genomeinfodb + r-genomicfeatures + r-genomicranges + r-graph + r-iranges + r-jsonlite + r-organismdbi + r-rcurl + r-rsamtools + r-rsqlite + r-rtracklayer + r-s4vectors + r-xml)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/AnnotationHubData") + (synopsis "Transform public data resources into Bioconductor data structures") + (description + "These recipes convert a wide variety and a growing number of public bioinformatic +data sets into easily-used standard Bioconductor data structures.") + (license license:artistic2.0))) + (define-public r-anvil (package (name "r-anvil")