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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: Thu, 02 Feb 2023 02:28:06 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 61220 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: <61220@debbugs.gnu.org> Cc: rekado@elephly.net X-Debbugs-Original-Xcc: rekado@elephly.net Received: via spool by 61220-submit@debbugs.gnu.org id=B61220.16753048499202 (code B ref 61220); Thu, 02 Feb 2023 02:28:06 +0000 Received: (at 61220) by debbugs.gnu.org; 2 Feb 2023 02:27:29 +0000 Received: from localhost ([127.0.0.1]:60224 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pNPJw-0002OH-R1 for submit@debbugs.gnu.org; Wed, 01 Feb 2023 21:27:29 -0500 Received: from b2062.mx.srv.dfn.de ([194.95.234.172]:42459) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pNPJt-0002MR-OZ for 61220@debbugs.gnu.org; Wed, 01 Feb 2023 21:27:27 -0500 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=1675304838; x=1677119239; bh=keD1tGsNedgKxXPAr6iHAvBwBqmpEnJA+vouOHkK97k=; b=D3FZxP0f+3py AmsXMhm+YSUjlj8GtM25/l8SAjRBI6xVTiZciMeapE2YkJGZSXAr+vfsY2wEf4Ox zgnp9Jt2TDQIt44aB9oLLTF5W8PiqCqJpT53SY1qpu4Vl2XVggHREKC3XzM3sjnR 0MQnX+gmzUryC+uUix8Nj23bbnUmMVU= 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 id 88E771606CA for <61220@debbugs.gnu.org>; Thu, 2 Feb 2023 03:27:18 +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 15.1.2507.17; Thu, 2 Feb 2023 03:27:12 +0100 From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Date: Thu, 2 Feb 2023 03:26:57 +0100 Message-ID: <20230202022657.67003-10-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.39.1 In-Reply-To: <20230202022657.67003-1-madalinionel.patrascu@mdc-berlin.de> References: <20230202022657.67003-1-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-14.0.0.3092-9.0.1002-27422.004 X-TM-AS-Result: No-10-0.214800-5.000000 X-TMASE-MatchedRID: 2wfub8HDRfP/R1NSMc2qCU7nLUqYrlslFIuBIWrdOePfUZT83lbkEDlU lx4PIvA7cKOSpdxu/RvR2Jk3kswrWCq+GZ9ZHxIhuW77/y896sj4uJ1REX4MHaMZvngJnzipCMm WJ6tUT+eJek9VNKq6xVhJV8dlFHDML/fdNahJQfrX3j/lf1V8LBqZh28Q6E3rU72YOAMDJjieAi CmPx4NwBnUJ0Ek6yhjxEHRux+uk8jfhP1xgyx3DL4+xFM37BUAINFGJVQaEaZ3+Cg2kxpAnXaru kmaNdZXqRZMiwqrIw290LZdnSs2p5Ep7cOTgjnF/yInuOzz8H/MmDWh9xmF49xSR7be7fnTFTs4 ljtt094P2K/+wkyxVzs7KL+6XFB4pSBl0hpeDh8= X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10-0.214800-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27422.004 X-TM-SNTS-SMTP: 30E8593F405BFCE441527E26D8F557D85D56E1A2B99C4583E4DF57B443CFDC602002: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-adacgh2): New variable. --- gnu/packages/bioconductor.scm | 44 +++++++++++++++++++++++++++++++++++ 1 file changed, 44 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index c509dffb4c..b351936cd8 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -31,6 +31,7 @@ (define-module (gnu packages bioconductor) #:use-module ((guix licenses) #:prefix license:) + #:use-module (guix gexp) #:use-module (guix packages) #:use-module (guix download) #:use-module (guix git-download) @@ -1800,6 +1801,49 @@ (define-public r-absseq ranking by fold-change and visualization.") (license license:gpl3+))) +(define-public r-adacgh2 + (package + (name "r-adacgh2") + (version "2.38.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "ADaCGH2" version)) + (sha256 + (base32 "0g9x3lnr56035wq9ijdcri4sz5pwj8184yxm415gmsxrii9xvpfd")))) + (properties `((upstream-name . "ADaCGH2"))) + (build-system r-build-system) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + (add-before 'configure 'set-PYTHONPATH + (lambda _ + (setenv "PYTHONPATH" + (string-append (getcwd) ":" + (getenv "GUIX_PYTHONPATH")))))))) + ;; This is needed by toMap.py script which is not compatible with python3 + (inputs (list python2-minimal)) + (propagated-inputs + (list r-acgh + r-bit + r-cluster + r-dnacopy + r-ff + r-glad + r-snapcgh + r-tilingarray + r-waveslim)) + (home-page "https://github.com/rdiaz02/adacgh2") + (synopsis "Big data analysis from aCGH experiments") + (description + "This package analysis and creates plotts of array @acronym{CGH, comparative +genomic hybridization} data. Also, it allows usage of @acronym{CBS, Circular +Binary Segementation}, wavelet-based smoothing, HMM, BioHMM, GLAD, CGHseg. Most +computations are parallelized (either via forking or with clusters, including MPI +and sockets clusters) and use ff for storing data.") + (license license:gpl3+))) + (define-public r-adam (package (name "r-adam")