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authorYifan Zhu <ifanzhu@foxmail.com>2017-10-11 20:42:55 -0500
committerChristoph Junghans <christoph.junghans@gmail.com>2017-10-11 19:42:55 -0600
commit01e104dfcb795b8ea7b31548dcfb1fa336f01370 (patch)
tree6165bd850395a856ff7f8766d0e69e481cf3e26d
parent670463e95ace9bd63337394711256eb7ce3d305f (diff)
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r-rsamtools: created new package (#5702)
-rw-r--r--var/spack/repos/builtin/packages/r-rsamtools/package.py50
1 files changed, 50 insertions, 0 deletions
diff --git a/var/spack/repos/builtin/packages/r-rsamtools/package.py b/var/spack/repos/builtin/packages/r-rsamtools/package.py
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+##############################################################################
+# 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')