From b84424e8790030e2428570cf1ddd94fb2b46657a Mon Sep 17 00:00:00 2001 From: Eric Date: Tue, 17 Apr 2018 14:45:10 -0500 Subject: bismark: Create new package (#7795) * bismark: Create new package * bismark: fix dependency types --- .../repos/builtin/packages/bismark/package.py | 54 ++++++++++++++++++++++ 1 file changed, 54 insertions(+) create mode 100644 var/spack/repos/builtin/packages/bismark/package.py (limited to 'var') diff --git a/var/spack/repos/builtin/packages/bismark/package.py b/var/spack/repos/builtin/packages/bismark/package.py new file mode 100644 index 0000000000..62cb5a0ce9 --- /dev/null +++ b/var/spack/repos/builtin/packages/bismark/package.py @@ -0,0 +1,54 @@ +############################################################################## +# 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 Bismark(Package): + """A tool to map bisulfite converted sequence reads and determine cytosine + methylation states""" + + homepage = "https://www.bioinformatics.babraham.ac.uk/projects/bismark" + url = "https://github.com/FelixKrueger/Bismark/archive/0.19.0.tar.gz" + + version('0.19.0', 'f403654aded77bf0d1dac1203867ded1') + version('0.18.2', '42334b7e3ed53ba246f30f1f846b4af8') + + depends_on('bowtie2', type='run') + depends_on('perl', type='run') + depends_on('samtools', type='run') + + def install(self, spec, prefix): + mkdirp(prefix.bin) + install('bam2nuc', prefix.bin) + install('bismark', prefix.bin) + install('bismark_genome_preparation', prefix.bin) + install('bismark_methylation_extractor', prefix.bin) + install('bismark2bedGraph', prefix.bin) + install('bismark2report', prefix.bin) + install('bismark2summary', prefix.bin) + install('coverage2cytosine', prefix.bin) + install('deduplicate_bismark', prefix.bin) + install('filter_non_conversion', prefix.bin) + install('NOMe_filtering', prefix.bin) -- cgit v1.2.3-70-g09d2