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| -rw-r--r-- | var/spack/repos/builtin/packages/r-genomicfeatures/package.py | 58 |
1 files changed, 58 insertions, 0 deletions
diff --git a/var/spack/repos/builtin/packages/r-genomicfeatures/package.py b/var/spack/repos/builtin/packages/r-genomicfeatures/package.py new file mode 100644 index 0000000000..e3ba959de6 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-genomicfeatures/package.py @@ -0,0 +1,58 @@ +############################################################################## +# 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 RGenomicfeatures(RPackage): + """A set of tools and methods for making and manipulating transcript + centric annotations. With these tools the user can easily download the + genomic locations of the transcripts, exons and cds of a given organism, + from either the UCSC Genome Browser or a BioMart database (more sources + will be supported in the future). This information is then stored in a + local database that keeps track of the relationship between transcripts, + exons, cds and genes. Flexible methods are provided for extracting the + desired features in a convenient format.""" + + homepage = "http://bioconductor.org/packages/GenomicFeatures/" + url = "https://git.bioconductor.org/packages/GenomicFeatures" + list_url = homepage + + version('1.28.5', git='https://git.bioconductor.org/packages/GenomicFeatures', commit='ba92381ae93cb1392dad5e6acfab8f6c1d744834') + + depends_on('r-biocgenerics', 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-annotationdbi', type=('build', 'run')) + depends_on('r-dbi', type=('build', 'run')) + depends_on('r-rsqlite', type=('build', 'run')) + depends_on('r-rcurl', type=('build', 'run')) + depends_on('r-xvector', type=('build', 'run')) + depends_on('r-biostrings', type=('build', 'run')) + depends_on('r-rtracklayer', type=('build', 'run')) + depends_on('r-biomart', type=('build', 'run')) + depends_on('r-biobase', type=('build', 'run')) + depends_on('r@3.4.0:3.4.9', when='@1.28.5') |