From 8c306b7b83cfa7debae20461d036631f0c9f6e5f Mon Sep 17 00:00:00 2001 From: Yifan Zhu Date: Tue, 24 Oct 2017 07:07:45 -0500 Subject: r-minfi: created new package (#5887) --- .../repos/builtin/packages/r-minfi/package.py | 63 ++++++++++++++++++++++ 1 file changed, 63 insertions(+) create mode 100644 var/spack/repos/builtin/packages/r-minfi/package.py diff --git a/var/spack/repos/builtin/packages/r-minfi/package.py b/var/spack/repos/builtin/packages/r-minfi/package.py new file mode 100644 index 0000000000..f94a87b4f8 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-minfi/package.py @@ -0,0 +1,63 @@ +############################################################################## +# Copyright (c) 2013-2017, 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/llnl/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 RMinfi(RPackage): + """Tools to analyze & visualize Illumina Infinium methylation arrays.""" + + homepage = "https://bioconductor.org/packages/minfi/" + url = "https://git.bioconductor.org/packages/minfi" + list_url = homepage + + version('1.22.1', git='https://git.bioconductor.org/packages/minfi', commit='b2faf84bcbb291e32d470a0e029450093527545b') + + depends_on('r-biocgenerics', type=('build', 'run')) + depends_on('r-genomicranges', type=('build', 'run')) + depends_on('r-summarizedexperiment', type=('build', 'run')) + depends_on('r-biostrings', type=('build', 'run')) + depends_on('r-bumphunter', type=('build', 'run')) + depends_on('r-s4vectors', type=('build', 'run')) + depends_on('r-genomeinfodb', type=('build', 'run')) + depends_on('r-biobase', type=('build', 'run')) + depends_on('r-iranges', type=('build', 'run')) + depends_on('r-beanplot', type=('build', 'run')) + depends_on('r-rcolorbrewer', type=('build', 'run')) + depends_on('r-lattice', type=('build', 'run')) + depends_on('r-nor1mix', type=('build', 'run')) + depends_on('r-siggenes', type=('build', 'run')) + depends_on('r-limma', type=('build', 'run')) + depends_on('r-preprocesscore', type=('build', 'run')) + depends_on('r-illuminaio', type=('build', 'run')) + depends_on('r-matrixstats', type=('build', 'run')) + depends_on('r-mclust', type=('build', 'run')) + depends_on('r-genefilter', type=('build', 'run')) + depends_on('r-nlme', type=('build', 'run')) + depends_on('r-reshape', type=('build', 'run')) + depends_on('r-mass', type=('build', 'run')) + depends_on('r-quadprog', type=('build', 'run')) + depends_on('r-data-table', type=('build', 'run')) + depends_on('r-geoquery', type=('build', 'run')) + depends_on('r@3.4.0:3.4.9', when='@1.22.1') -- cgit v1.2.3-70-g09d2