r-aldex2: Create new package. (#6015)

1 files changed, 51 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/r-aldex2/package.py b/var/spack/repos/builtin/packages/r-aldex2/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 RAldex2(RPackage):
+    """A differential abundance analysis for the comparison of
+    two or more conditions. For example, single-organism and
+    meta-RNA-seq high-throughput sequencing assays, or of
+    selected and unselected values from in-vitro sequence selections.
+    Uses a Dirichlet-multinomial model to infer abundance from counts,
+    that has been optimized for three or more experimental replicates.
+    Infers sampling variation and calculates the expected false
+    discovery rate given the biological and sampling variation
+    using the Wilcox rank test or Welches t-test (aldex.ttest) or
+    the glm and Kruskal Wallis tests (aldex.glm). Reports both P
+    and fdr values calculated by the Benjamini Hochberg correction."""
+
+    homepage = "http://bioconductor.org/packages/ALDEx2/"
+    url      = "https://git.bioconductor.org/packages/ALDEx2"
+
+    version('1.8.0', git='https://git.bioconductor.org/packages/ALDEx2', commit='24104824ca2402ad4f54fbf1ed9cee7fac2aaaf1')
+
+    depends_on('r@3.4.0:3.4.9', when='@1.8.0')
+    depends_on('r-s4vectors', type=('build', 'run'))
+    depends_on('r-iranges', type=('build', 'run'))
+    depends_on('r-genomicranges', type=('build', 'run'))
+    depends_on('r-summarizedexperiment', type=('build', 'run'))
+    depends_on('r-biocparallel', type=('build', 'run'))