r-edger: created new package (#5571)

1 files changed, 44 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/r-edger/package.py b/var/spack/repos/builtin/packages/r-edger/package.py
new file mode 100644
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+++ b/var/spack/repos/builtin/packages/r-edger/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 REdger(RPackage):
+    """Differential expression analysis of RNA-seq expression profiles with
+       biological replication. Implements a range of statistical methodology
+       based on the negative binomial distributions, including empirical Bayes
+       estimation, exact tests, generalized linear models and quasi-likelihood
+       tests. As well as RNA-seq, it be applied to differential signal analysis
+       of other types of genomic data that produce counts, including ChIP-seq,
+       SAGE and CAGE."""
+
+    homepage = "https://bioconductor.org/packages/edgeR/"
+    url      = "https://bioconductor.org/packages/3.5/bioc/src/contrib/edgeR_3.18.1.tar.gz"
+    list_url = homepage
+
+    version('3.18.1', 'f074fe4d8f220efe27d61c0666e4b270')
+
+    depends_on('r-limma', type=('build', 'run'))
+    depends_on('r-locfit', type=('build', 'run'))