From 10fcd9382acc95d76c02fbc793da7edef1a28798 Mon Sep 17 00:00:00 2001 From: Yifan Zhu Date: Tue, 31 Oct 2017 17:17:07 -0500 Subject: r-ggbio: new package (#6058) --- .../repos/builtin/packages/r-ggbio/package.py | 69 ++++++++++++++++++++++ 1 file changed, 69 insertions(+) create mode 100644 var/spack/repos/builtin/packages/r-ggbio/package.py (limited to 'var') diff --git a/var/spack/repos/builtin/packages/r-ggbio/package.py b/var/spack/repos/builtin/packages/r-ggbio/package.py new file mode 100644 index 0000000000..56a26b4a9f --- /dev/null +++ b/var/spack/repos/builtin/packages/r-ggbio/package.py @@ -0,0 +1,69 @@ +############################################################################## +# 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 RGgbio(RPackage): + """The ggbio package extends and specializes the grammar of graphics for + biological data. The graphics are designed to answer common scientific + questions, in particular those often asked of high throughput genomics + data. All core Bioconductor data structures are supported, where + appropriate. The package supports detailed views of particular genomic + regions, as well as genome-wide overviews. Supported overviews include + ideograms and grand linear views. High-level plots include sequence + fragment length, edge-linked interval to data view, mismatch pileup, + and several splicing summaries.""" + + homepage = "http://bioconductor.org/packages/ggbio/" + url = "https://git.bioconductor.org/packages/ggbio" + list_url = homepage + + version('1.24.1', git='https://git.bioconductor.org/packages/ggbio', commit='ef04c1bca1330f37152bcc21080cbde94849a094') + + depends_on('r-gridextra', type=('build', 'run')) + depends_on('r-scales', type=('build', 'run')) + depends_on('r-reshape2', type=('build', 'run')) + depends_on('r-gtable', type=('build', 'run')) + depends_on('r-hmisc', type=('build', 'run')) + depends_on('r-biovizbase', type=('build', 'run')) + depends_on('r-biobase', type=('build', 'run')) + depends_on('r-s4vectors', type=('build', 'run')) + depends_on('r-iranges', type=('build', 'run')) + depends_on('r-genomeinfodb', 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-rsamtools', type=('build', 'run')) + depends_on('r-genomicalignments', type=('build', 'run')) + depends_on('r-bsgenome', type=('build', 'run')) + depends_on('r-variantannotation', type=('build', 'run')) + depends_on('r-rtracklayer', type=('build', 'run')) + depends_on('r-genomicfeatures', type=('build', 'run')) + depends_on('r-organismdbi', type=('build', 'run')) + depends_on('r-ggally', type=('build', 'run')) + depends_on('r-ensembldb', type=('build', 'run')) + depends_on('r-annotationdbi', type=('build', 'run')) + depends_on('r-annotationfilter', type=('build', 'run')) + depends_on('r@3.4.0:3.4.9', when='@1.24.1') -- cgit v1.2.3-70-g09d2