diff options
| -rw-r--r-- | var/spack/repos/builtin/packages/r-bamsignals/package.py | 45 |
1 files changed, 45 insertions, 0 deletions
diff --git a/var/spack/repos/builtin/packages/r-bamsignals/package.py b/var/spack/repos/builtin/packages/r-bamsignals/package.py new file mode 100644 index 0000000000..29a7fda80d --- /dev/null +++ b/var/spack/repos/builtin/packages/r-bamsignals/package.py @@ -0,0 +1,45 @@ +############################################################################## +# 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 RBamsignals(RPackage): + """This package allows to efficiently obtain count vectors + from indexed bam files. It counts the number of reads in given + genomic ranges and it computes reads profiles and coverage + profiles. It also handles paired-end data.""" + + homepage = "https://www.bioconductor.org/packages/bamsignals/" + url = "https://git.bioconductor.org/packages/bamsignals" + + version('1.8.0', git='https://git.bioconductor.org/packages/bamsignals', commit='b123b83e8e026c9ec91209d4498aff3e95a5de23') + + depends_on('r@3.4.0:3.4.9', when='@1.8.0') + depends_on('r-biocgenerics', type=('build', 'run')) + depends_on('r-rcpp', type=('build', 'run')) + depends_on('r-iranges', type=('build', 'run')) + depends_on('r-genomicranges', type=('build', 'run')) + depends_on('r-zlibbioc', type=('build', 'run')) + depends_on('r-rhtslib', type=('build', 'run')) |