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# Copyright 2013-2024 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.package import *
class Bsseeker2(Package):
"""A versatile aligning pipeline for bisulfite sequencing data."""
homepage = "http://pellegrini.mcdb.ucla.edu/BS_Seeker2"
url = "https://github.com/BSSeeker/BSseeker2/archive/BSseeker2-v2.1.8.tar.gz"
license("MIT")
version("2.1.8", sha256="34ebedce36a0fca9e22405d4c2c20bc978439d4a34d1d543657fbc53ff847934")
version(
"2.1.7",
sha256="ac90fb4ad8853ee920f1ffea2b1a8cfffcdb1508ff34be0091d5a9c90ac8c74a",
url="https://github.com/BSSeeker/BSseeker2/archive/v2.1.7.tar.gz",
)
version(
"2.1.2",
sha256="08055dd314f85a9b74c259c2cb894ea2affdab2c7a120af3589c649e1900c5c6",
url="https://github.com/BSSeeker/BSseeker2/archive/v2.1.2.tar.gz",
)
depends_on("python@2.6:", type=("build", "run"))
depends_on("py-pysam", type=("build", "run"))
def install(self, spec, prefix):
mkdirp(prefix.bin)
install("Antisense.py", prefix.bin)
install_tree("bs_index", prefix.bin.bs_index)
install("bs_seeker2-build.py", prefix.bin)
install_tree("bs_utils", prefix.bin.bs_utils)
install_tree("galaxy", prefix.bin.galaxy)
install_tree("bs_align", prefix.bin.bs_align)
install("bs_seeker2-align.py", prefix.bin)
install("bs_seeker2-call_methylation.py", prefix.bin)
install("FilterReads.py", prefix.bin)
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