From patchwork Wed Oct 30 10:25:31 2019 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Simon Tournier X-Patchwork-Id: 15895 Return-Path: X-Original-To: patchwork@mira.cbaines.net Delivered-To: patchwork@mira.cbaines.net Received: by mira.cbaines.net (Postfix, from userid 113) id 5FBBC17685; Wed, 30 Oct 2019 10:26:18 +0000 (GMT) X-Spam-Checker-Version: SpamAssassin 3.4.0 (2014-02-07) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-1.9 required=5.0 tests=BAYES_00,FREEMAIL_FROM, RCVD_IN_MSPIKE_H2,T_DKIM_INVALID,URIBL_BLOCKED autolearn=unavailable autolearn_force=no version=3.4.0 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTP id 18DDD17674 for ; Wed, 30 Oct 2019 10:26:18 +0000 (GMT) Received: from localhost ([::1]:38700 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1iPlBB-0007Um-Cs for patchwork@mira.cbaines.net; Wed, 30 Oct 2019 06:26:17 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:40274) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1iPlB0-0007QZ-0D for guix-patches@gnu.org; Wed, 30 Oct 2019 06:26:07 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1iPlAy-0002ld-KZ for guix-patches@gnu.org; Wed, 30 Oct 2019 06:26:05 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:40481) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1iPlAy-0002lA-Fr for guix-patches@gnu.org; Wed, 30 Oct 2019 06:26:04 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1iPlAx-0005W1-PU for guix-patches@gnu.org; Wed, 30 Oct 2019 06:26:04 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#37988] [PATCH 6/6] gnu: Add r-flowworkspace. Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Wed, 30 Oct 2019 10:26:03 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 37988 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 37988@debbugs.gnu.org Cc: zimoun Received: via spool by 37988-submit@debbugs.gnu.org id=B37988.157243116021158 (code B ref 37988); Wed, 30 Oct 2019 10:26:03 +0000 Received: (at 37988) by debbugs.gnu.org; 30 Oct 2019 10:26:00 +0000 Received: from localhost ([127.0.0.1]:49294 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1iPlAu-0005V6-51 for submit@debbugs.gnu.org; Wed, 30 Oct 2019 06:26:00 -0400 Received: from mail-wr1-f68.google.com ([209.85.221.68]:41219) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1iPlAj-0005UA-HR for 37988@debbugs.gnu.org; Wed, 30 Oct 2019 06:25:52 -0400 Received: by mail-wr1-f68.google.com with SMTP id p4so1633895wrm.8 for <37988@debbugs.gnu.org>; Wed, 30 Oct 2019 03:25:49 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=from:to:cc:subject:date:message-id:in-reply-to:references :mime-version:content-transfer-encoding; bh=M0rGms2nvbWS20tLFPIynEvDoGLaGhMxz3isshnakiA=; b=gjsSQyQjI7tclSqkDplypyrzcLqNY4GN2mtG+vDjZyuOZURF6LlFOP3FAeWoJdvqnt 60POUtQk7Vz/2Bkxo1jMxwHAEHGI7LFcaDXK3mMH2CNG3YgeCTEsJP8CDQ34fGOaCyYL gDCjxo4gLC4jtiSGHcN8BsCuJo9xhtsv9Ei9Io0F2SCL/ibwMFCzpE2kj/Uu1PPLG6U0 y5Mmv2c1xdJCUzclQUKjOl+HEPhF8BE1L5Rf12LfLkFXRrBNERhPzZdPHFH9vI0MJEH8 lEyFUJpEiwRIbqGkQ9DfW4n21Ocs3cf5+kNJiwGh8/nIpNkCpyuDAonT0CNg36avgPGO FU0Q== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:from:to:cc:subject:date:message-id:in-reply-to :references:mime-version:content-transfer-encoding; bh=M0rGms2nvbWS20tLFPIynEvDoGLaGhMxz3isshnakiA=; b=aB+zPXwe5IootGzGUsHh3NO92HXSfIkx7cYE4QY6NS51nSMaTrzgbm53Sf7xBepXeS mCyQ5EwiHPIheXc0Qi1tjWH8OWOrhLXN0mW5/Ig+tVYoNib3Kioh8h90yEZ4JOEXY5Lm z85Lur4JTQfRy+1uKa3VBfA/WPli9lqDZPMYJ9aA5Iv5FNuP2aMZZp2w68X9OvshrafB AY7ddId9ANEovgiEZTZTCXsHjbKjYyQVao4OPqFmQXqGzzH3AaYmYe4qKmqEqWf6Xzss 41B0jBpFqoEHGXf2l1gTjqH2G/d5xI9cPr5G3Z725KdNgMFRQF3GLenwBSu08Sznh16n qsIw== X-Gm-Message-State: APjAAAUU487F1tuHITxjB2yG8fJrmspq82bJUZP84sojXRQn/pyy10Mz KXBXSA+Lmu5lOj3z8NzAGeGJCFkK X-Google-Smtp-Source: APXvYqzEXQzBD6ORavqs/MGBtKWXqG/+HjoSEt61N12QO3Iz9yTqdn16lfEbsBX0VNcXrA5XOe2OmA== X-Received: by 2002:adf:f547:: with SMTP id j7mr5580227wrp.69.1572431143799; Wed, 30 Oct 2019 03:25:43 -0700 (PDT) Received: from pfiuh02.univ-paris-diderot.fr ([193.48.40.241]) by smtp.gmail.com with ESMTPSA id x205sm2493321wmb.5.2019.10.30.03.25.43 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Wed, 30 Oct 2019 03:25:43 -0700 (PDT) From: zimoun Date: Wed, 30 Oct 2019 11:25:31 +0100 Message-Id: <20191030102531.12495-6-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.23.0 In-Reply-To: <20191030102531.12495-1-zimon.toutoune@gmail.com> References: <20191030102531.12495-1-zimon.toutoune@gmail.com> MIME-Version: 1.0 X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] X-Received-From: 209.51.188.43 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" X-getmail-retrieved-from-mailbox: Patches * gnu/packages/bioconductor.scm (r-flowworkspace): New variable. --- gnu/packages/bioconductor.scm | 50 +++++++++++++++++++++++++++++++++++ 1 file changed, 50 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 2636095e0f..dabfcb2cb3 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6260,3 +6260,53 @@ represent and interact with the gated cytometry data.") "This package provides HDF5 storage based methods and functions for manipulation of flow cytometry data.") (license license:artistic2.0))) + +(define-public r-flowworkspace + (package + (name "r-flowworkspace") + (version "3.32.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "flowWorkspace" version)) + (sha256 + (base32 + "1r1xxqzlp2x2gf79f37ckninnyjkxcb7xz7rffg2nadmapl5shvw")))) + (properties + `((upstream-name . "flowWorkspace"))) + (build-system r-build-system) + (propagated-inputs + `(("r-bh" ,r-bh) + ("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-cytolib" ,r-cytolib) + ("r-data-table" ,r-data-table) + ("r-digest" ,r-digest) + ("r-dplyr" ,r-dplyr) + ("r-flowcore" ,r-flowcore) + ("r-flowviz" ,r-flowviz) + ("r-graph" ,r-graph) + ("r-gridextra" ,r-gridextra) + ("r-lattice" ,r-lattice) + ("r-latticeextra" ,r-latticeextra) + ("r-matrixstats" ,r-matrixstats) + ("r-ncdfflow" ,r-ncdfflow) + ("r-rbgl" ,r-rbgl) + ("r-rcolorbrewer" ,r-rcolorbrewer) + ("r-rcpp" ,r-rcpp) + ("r-rcppparallel" ,r-rcppparallel) + ("r-rgraphviz" ,r-rgraphviz) + ("r-rprotobuflib" ,r-rprotobuflib) + ("r-scales" ,r-scales) + ("r-stringr" ,r-stringr))) + (home-page + "https://bioconductor.org/packages/flowWorkspace") + (synopsis "Infrastructure for representing and interacting with cytometry data sets") + (description + "This package provides importer for basic workspaces from the proprietary +software FlowJo into the BioConductor package flowCore. It is designed to +facilitate comparison of automated gating methods against manual gating. +Gating hierarchies, groups of samples, compensation, and transformation are +performed so that the output matches the analysis from the proprietary +software FlowJo.") + (license license:artistic2.0)))