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# Copyright 2013-2023 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)
import os
from spack.package import *
class Bracken(Package):
"""Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly
accurate statistical method that computes the abundance of species in DNA
sequences from a metagenomics sample."""
homepage = "https://ccb.jhu.edu/software/bracken"
url = "https://github.com/jenniferlu717/Bracken/archive/v2.7.tar.gz"
license("GPL-3.0-only")
version("2.8", sha256="b0c8a803cc020b7d1cbca47b53e71e874d9688b836911e4a4b71b0e4b826b61a")
version("2.7", sha256="1795ecd9f9e5582f37549795ba68854780936110a2f6f285c3e626d448cd1532")
depends_on("python", type="run")
depends_on("kraken2", type="run")
def install(self, spec, prefix):
mkdirp(prefix.bin.src)
# installer builds kmer2read_distr in src
chmod = which("chmod")
chmod("+x", "./install_bracken.sh")
installer = Executable("./install_bracken.sh")
installer(self.stage.source_path)
# move main scripts to bin
install("bracken", prefix.bin)
install("bracken-build", prefix.bin)
install("./src/kmer2read_distr", prefix.bin)
install("./analysis_scripts/combine_bracken_outputs.py", prefix.bin)
chmod("+x", join_path(prefix.bin, "combine_bracken_outputs.py"))
# move scripts to src and create symlinks
files = ("est_abundance.py", "generate_kmer_distribution.py")
for file in files:
filepath = join_path("./src", file)
if os.path.isfile(filepath):
install(filepath, prefix.bin.src)
symlink(join_path(prefix.bin.src, file), join_path(prefix.bin, file))
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