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Diffstat (limited to 'var')
| -rw-r--r-- | var/spack/repos/builtin/packages/r-shortread/package.py | 55 |
1 files changed, 55 insertions, 0 deletions
diff --git a/var/spack/repos/builtin/packages/r-shortread/package.py b/var/spack/repos/builtin/packages/r-shortread/package.py new file mode 100644 index 0000000000..b2625916c8 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-shortread/package.py @@ -0,0 +1,55 @@ +############################################################################## +# 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/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 RShortread(RPackage): + """This package implements sampling, iteration, and input of FASTQ + files. The package includes functions for filtering and trimming + reads, and for generating a quality assessment report. Data are + represented as DNAStringSet-derived objects, and easily manipulated + for a diversity of purposes. The package also contains legacy support + for early single-end, ungapped alignment formats.""" + + homepage = "https://www.bioconductor.org/packages/ShortRead/" + url = "https://git.bioconductor.org/packages/ShortRead" + + version('1.34.2', git='https://git.bioconductor.org/packages/ShortRead', commit='25daac63b301df66a8ef6e98cc2977522c6786cd') + + depends_on('r@3.4.0:3.4.9', when='@1.34.2') + depends_on('r-latticeextra', type=('build', 'run')) + depends_on('r-lattice', type=('build', 'run')) + depends_on('r-zlibbioc', type=('build', 'run')) + depends_on('r-hwriter', type=('build', 'run')) + depends_on('r-genomicranges', type=('build', 'run')) + depends_on('r-genomeinfodb', type=('build', 'run')) + depends_on('r-iranges', type=('build', 'run')) + depends_on('r-s4vectors', type=('build', 'run')) + depends_on('r-biobase', type=('build', 'run')) + depends_on('r-genomicalignments', type=('build', 'run')) + depends_on('r-rsamtools', type=('build', 'run')) + depends_on('r-biostrings', type=('build', 'run')) + depends_on('r-biocparallel', type=('build', 'run')) + depends_on('r-biocgenerics', type=('build', 'run')) |