From 22f91251642e0a57bf73d63d4d546c56278ffd13 Mon Sep 17 00:00:00 2001 From: Yifan Zhu Date: Mon, 30 Oct 2017 23:39:54 -0500 Subject: r-ensembldb: created new package (#6038) --- .../repos/builtin/packages/r-ensembldb/package.py | 62 ++++++++++++++++++++++ 1 file changed, 62 insertions(+) create mode 100644 var/spack/repos/builtin/packages/r-ensembldb/package.py (limited to 'var') diff --git a/var/spack/repos/builtin/packages/r-ensembldb/package.py b/var/spack/repos/builtin/packages/r-ensembldb/package.py new file mode 100644 index 0000000000..0439f60019 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-ensembldb/package.py @@ -0,0 +1,62 @@ +############################################################################## +# 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 REnsembldb(RPackage): + """The package provides functions to create and use transcript centric + annotation databases/packages. The annotation for the databases are + directly fetched from Ensembl using their Perl API. The functionality + and data is similar to that of the TxDb packages from the + GenomicFeatures package, but, in addition to retrieve all + gene/transcript models and annotations from the database, the ensembldb + package provides also a filter framework allowing to retrieve + annotations for specific entries like genes encoded on a chromosome + region or transcript models of lincRNA genes.""" + + homepage = "https://bioconductor.org/packages/ensembldb/" + url = "https://git.bioconductor.org/packages/ensembldb" + list_url = homepage + + version('2.0.4', git='https://git.bioconductor.org/packages/ensembldb', commit='514623d71e3cca7a4e547adb579b5a958702ef86') + + depends_on('r-biocgenerics', type=('build', 'run')) + depends_on('r-genomicranges', type=('build', 'run')) + depends_on('r-genomicfeatures', type=('build', 'run')) + depends_on('r-annotationfilter', type=('build', 'run')) + depends_on('r-rsqlite', type=('build', 'run')) + depends_on('r-dbi', type=('build', 'run')) + depends_on('r-biobase', type=('build', 'run')) + depends_on('r-genomeinfodb', type=('build', 'run')) + depends_on('r-annotationdbi', type=('build', 'run')) + depends_on('r-rtracklayer', type=('build', 'run')) + depends_on('r-s4vectors', type=('build', 'run')) + depends_on('r-annotationhub', type=('build', 'run')) + depends_on('r-rsamtools', type=('build', 'run')) + depends_on('r-iranges', type=('build', 'run')) + depends_on('r-protgenerics', type=('build', 'run')) + depends_on('r-biostrings', type=('build', 'run')) + depends_on('r-curl', type=('build', 'run')) + depends_on('r@3.4.0:3.4.9', type=('build', 'run')) -- cgit v1.2.3-70-g09d2