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authorYifan Zhu <ifanzhu@foxmail.com>2017-10-25 04:17:15 -0500
committerTodd Gamblin <tgamblin@llnl.gov>2017-10-25 11:17:15 +0200
commitf87c426a6c29651e4183b8613237004b99f8abae (patch)
treefcc797a82146276fb90b7cc478e795c95532a47e
parentf1c06dec7c1cf05860e999d974145c24297fc211 (diff)
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r-variantannotation: created new package (#5932)
-rw-r--r--var/spack/repos/builtin/packages/r-variantannotation/package.py54
1 files changed, 54 insertions, 0 deletions
diff --git a/var/spack/repos/builtin/packages/r-variantannotation/package.py b/var/spack/repos/builtin/packages/r-variantannotation/package.py
new file mode 100644
index 0000000000..0ad9605a5b
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+++ b/var/spack/repos/builtin/packages/r-variantannotation/package.py
@@ -0,0 +1,54 @@
+##############################################################################
+# 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 RVariantannotation(RPackage):
+ """Annotate variants, compute amino acid coding changes, predict coding
+ outcomes."""
+
+ homepage = "https://www.bioconductor.org/packages/VariantAnnotation/"
+ url = "https://git.bioconductor.org/packages/VariantAnnotation"
+ list_url = homepage
+
+ version('1.22.3', git='https://git.bioconductor.org/packages/VariantAnnotation', commit='3a91b6d4297aa416d5f056dec6f8925eb1a8eaee')
+
+ depends_on('r-biocgenerics', type=('build', 'run'))
+ depends_on('r-genomeinfodb', type=('build', 'run'))
+ depends_on('r-genomicranges', type=('build', 'run'))
+ depends_on('r-summarizedexperiment', type=('build', 'run'))
+ depends_on('r-rsamtools', type=('build', 'run'))
+ depends_on('r-dbi', type=('build', 'run'))
+ depends_on('r-zlibbioc', type=('build', 'run'))
+ depends_on('r-biobase', 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-biostrings', type=('build', 'run'))
+ depends_on('r-annotationdbi', type=('build', 'run'))
+ depends_on('r-bsgenome', type=('build', 'run'))
+ depends_on('r-rtracklayer', type=('build', 'run'))
+ depends_on('r-genomicfeatures', type=('build', 'run'))
+ depends_on('r@3.4.0:3.4.9', when='@1.22.3')