r-tfbstools: new package (#7243)

1 files changed, 68 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/r-tfbstools/package.py b/var/spack/repos/builtin/packages/r-tfbstools/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/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 RTfbstools(RPackage):
+    """TFBSTools is a package for the analysis and manipulation of
+       transcription factor binding sites.
+
+       It includes matrices conversion between Position Frequency Matirx (PFM),
+       Position Weight Matirx (PWM) and Information Content Matrix (ICM). It
+       can also scan putative TFBS from sequence/alignment, query JASPAR
+       database and provides a wrapper of de novo motif discovery software.
+       TFBSTools is a package for the analysis and manipulation of
+       transcription factor binding sites. It includes matrices conversion
+       between Position Frequency Matirx (PFM), Position Weight Matirx (PWM)
+       and Information Content Matrix (ICM). It can also scan putative TFBS
+       from sequence/alignment, query JASPAR database and provides a wrapper
+       of de novo motif discovery software."""
+
+    homepage = "http://bioconductor.org/packages/TFBSTools/"
+    url      = "https://git.bioconductor.org/packages/TFBSTools"
+
+    version('1.16.0', git='https://git.bioconductor.org/packages/TFBSTools', commit='565436a5a674d4dea7279e796a20c5bd2034f65a')
+
+    depends_on('r-biobase@2.28:', type=('build', 'run'))
+    depends_on('r-biostrings@2.36.4:', type=('build', 'run'))
+    depends_on('r-biocgenerics@0.14.0:', type=('build', 'run'))
+    depends_on('r-biocparallel@1.2.21:', type=('build', 'run'))
+    depends_on('r-bsgenome@1.36.3:', type=('build', 'run'))
+    depends_on('r-catools@1.17.1:', type=('build', 'run'))
+    depends_on('r-cner@1.4.0:', type=('build', 'run'))
+    depends_on('r-dirichletmultinomial@1.10.0:', type=('build', 'run'))
+    depends_on('r-genomeinfodb@1.6.1:', type=('build', 'run'))
+    depends_on('r-genomicranges@1.20.6:', type=('build', 'run'))
+    depends_on('r-gtools@3.5.0:', type=('build', 'run'))
+    depends_on('r-iranges@2.2.7:', type=('build', 'run'))
+    depends_on('r-dbi@0.6:', type=('build', 'run'))
+    depends_on('r-rsqlite@1.0.0:', type=('build', 'run'))
+    depends_on('r-rtracklayer@1.28.10:', type=('build', 'run'))
+    depends_on('r-seqlogo@1.34.0:', type=('build', 'run'))
+    depends_on('r-s4vectors@0.9.25:', type=('build', 'run'))
+    depends_on('r-tfmpvalue@0.0.5:', type=('build', 'run'))
+    depends_on('r-xml@3.98-1.3:', type=('build', 'run'))
+    depends_on('r-xvector@0.8.0:', type=('build', 'run'))
+    depends_on('r@3.4.3:3.4.9', when='@1.16.0')