36 lines
1.4 KiB
Python
36 lines
1.4 KiB
Python
# Copyright 2013-2020 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', sha256='91707737f96a0574956a282b635abad7560e7d90bee188a67a7807b2470deae2')
|
|
version('0.18.2', sha256='83391c5b5af33047178e7774ac25f5a69ce9315c13ae02f016baf7c50b73e702')
|
|
|
|
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)
|