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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)
from spack.package import *
class Shortbred(Package):
"""ShortBRED is a system for profiling protein families of interest at
very high specificity in shotgun meta'omic sequencing data."""
homepage = "https://huttenhower.sph.harvard.edu/shortbred"
url = "https://bitbucket.org/biobakery/shortbred/get/0.9.4.tar.gz"
version(
"0.9.4",
sha256="a85e5609db79696d3f2d478408fc6abfeea7628de9f533c4e1e0ea3622b397ba",
deprecated=True,
)
depends_on("blast-plus@2.2.28:")
depends_on("cdhit@4.6:")
depends_on("muscle@3.8.31:")
depends_on("python@2.7.9:")
depends_on("py-biopython")
depends_on("usearch@6.0.307:")
def install(self, spec, prefix):
mkdirp(prefix.bin)
install("shortbred_identify.py", prefix.bin)
install("shortbred_quantify.py", prefix.bin)
install_tree("src", prefix.src)
def setup_run_environment(self, env):
env.prepend_path("PYTHONPATH", self.prefix)
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