From 01e104dfcb795b8ea7b31548dcfb1fa336f01370 Mon Sep 17 00:00:00 2001 From: Yifan Zhu Date: Wed, 11 Oct 2017 20:42:55 -0500 Subject: r-rsamtools: created new package (#5702) --- .../repos/builtin/packages/r-rsamtools/package.py | 50 ++++++++++++++++++++++ 1 file changed, 50 insertions(+) create mode 100644 var/spack/repos/builtin/packages/r-rsamtools/package.py (limited to 'var') diff --git a/var/spack/repos/builtin/packages/r-rsamtools/package.py b/var/spack/repos/builtin/packages/r-rsamtools/package.py new file mode 100644 index 0000000000..45c0286495 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-rsamtools/package.py @@ -0,0 +1,50 @@ +############################################################################## +# 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 RRsamtools(RPackage): + """This package provides an interface to the 'samtools', 'bcftools', and + 'tabix' utilities (see 'LICENCE') for manipulating SAM (Sequence + Alignment / Map), FASTA, binary variant call (BCF) and compressed + indexed tab-delimited (tabix) files.""" + + homepage = "https://bioconductor.org/packages/Rsamtools/" + url = "https://bioconductor.org/packages/3.5/bioc/src/contrib/Rsamtools_1.28.0.tar.gz" + list_url = homepage + + version('1.28.0', '313bceac68edec07f2ee466520461d35') + + depends_on('r-genomeinfodb', type=('build', 'run')) + depends_on('r-genomicranges', type=('build', 'run')) + depends_on('r-biostrings', type=('build', 'run')) + depends_on('r-biocgenerics', type=('build', 'run')) + depends_on('r-s4vectors', type=('build', 'run')) + depends_on('r-iranges', type=('build', 'run')) + depends_on('r-xvector', type=('build', 'run')) + depends_on('r-zlibbioc', type=('build', 'run')) + depends_on('r-bitops', type=('build', 'run')) + depends_on('r-biocparallel', type=('build', 'run')) + depends_on('r@3.4.0:3.4.9', when='@1.28.0') -- cgit v1.2.3-60-g2f50