r-rtracklayer: new package (#5808)

1 files changed, 53 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/r-rtracklayer/package.py b/var/spack/repos/builtin/packages/r-rtracklayer/package.py
new file mode 100644
index 0000000000..7aa171b129
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-rtracklayer/package.py
@@ -0,0 +1,53 @@
+##############################################################################
+# 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 RRtracklayer(RPackage):
+    """Extensible framework for interacting with multiple genome browsers
+       (currently UCSC built-in) and manipulating annotation tracks in various
+       formats (currently GFF, BED, bedGraph, BED15, WIG, BigWig and 2bit
+       built-in). The user may export/import tracks to/from the supported
+       browsers, as well as query and modify the browser state, such as the
+       current viewport."""
+
+    homepage = "http://bioconductor.org/packages/rtracklayer/"
+    url      = "https://git.bioconductor.org/packages/rtracklayer"
+    list_url = homepage
+
+    version('1.36.6', git='https://git.bioconductor.org/packages/rtracklayer', commit='8c0ac7230f94e0c5a981acbb178c8de70e968131')
+
+    depends_on('r-xml', 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-genomeinfodb', type=('build', 'run'))
+    depends_on('r-biostrings', type=('build', 'run'))
+    depends_on('r-zlibbioc', type=('build', 'run'))
+    depends_on('r-rcurl', type=('build', 'run'))
+    depends_on('r-rsamtools', type=('build', 'run'))
+    depends_on('r-genomicalignments', type=('build', 'run'))
+    depends_on('r@3.4.0:3.4.9', when='@1.36.6')