hlrs-software-stack/spack
7
0
Fork 0
Code Issues Pull requests Projects Releases Packages Wiki Activity

r-tfbstools: new package (#7243)

Browse source
This commit is contained in:
Yifan Zhu 2018-03-13 06:40:41 -05:00 committed by Massimiliano Culpo
parent 6f76c2124a
commit 5bd8ec8160
1 changed files with 68 additions and 0 deletions
Show stats Download patch file Download diff file Expand all files Collapse all files

68
var/spack/repos/builtin/packages/r-tfbstools/package.py Normal file
View file

@ -0,0 +1,68 @@
##############################################################################
# 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')