From 7fd6291d59d184cd06dfbe702559562460d04f15 Mon Sep 17 00:00:00 2001 From: Levi Baber Date: Mon, 13 Aug 2018 22:20:41 -0500 Subject: r-glimma: new package (#8940) * r-glimma: new package * r-glimma: git not url * r-glimma: adding runtime deps * r-glimma: dep types --- .../repos/builtin/packages/r-glimma/package.py | 43 ++++++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 var/spack/repos/builtin/packages/r-glimma/package.py diff --git a/var/spack/repos/builtin/packages/r-glimma/package.py b/var/spack/repos/builtin/packages/r-glimma/package.py new file mode 100644 index 0000000000..768d94bbe1 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-glimma/package.py @@ -0,0 +1,43 @@ +############################################################################## +# Copyright (c) 2013-2018, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/spack/spack +# Please also see the NOTICE and LICENSE files for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class RGlimma(RPackage): + """This package generates interactive visualisations for analysis of + RNA-sequencing data using output from limma, edgeR or DESeq2 packages + in an HTML page. The interactions are built on top of the popular + static representations of analysis results in order to provide + additional information.""" + + homepage = "https://bioconductor.org/packages/release/bioc/html/Glimma.html" + git = "https://git.bioconductor.org/packages/Glimma.git" + + version('1.8.2', commit='f4aa1f05c2890d04b01ad4c0ab27f2f729f2c969') + + depends_on('r@3.5.0:3.5.9', when='@1.8.2:', type=('build', 'run')) + depends_on('r-edger', type=('build', 'run')) + depends_on('r-jsonlite', type=('build', 'run')) + depends_on('r-s4vectors', type=('build', 'run')) -- cgit v1.2.3-70-g09d2