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Diffstat (limited to 'var/spack/repos/builtin/packages/bismark/package.py')
| -rw-r--r-- | var/spack/repos/builtin/packages/bismark/package.py | 35 |
1 files changed, 35 insertions, 0 deletions
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..4326c63fc6 --- /dev/null +++ b/var/spack/repos/builtin/packages/bismark/package.py @@ -0,0 +1,35 @@ +# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +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) |