From ed656dccf5aeff6bdc7449c38cd833555052fdab Mon Sep 17 00:00:00 2001 From: Yifan Zhu Date: Tue, 3 Oct 2017 18:34:46 -0500 Subject: [PATCH] r-edger: created new package (#5571) --- .../repos/builtin/packages/r-edger/package.py | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 var/spack/repos/builtin/packages/r-edger/package.py 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 index 0000000000..7b871ed56f --- /dev/null +++ b/var/spack/repos/builtin/packages/r-edger/package.py @@ -0,0 +1,44 @@ +############################################################################## +# 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'))