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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.path
from spack.package import *
class Ampliconnoise(MakefilePackage):
"""AmpliconNoise is a collection of programs for the removal of noise
from 454 sequenced PCR amplicons."""
homepage = "https://directory.fsf.org/wiki/AmpliconNoise"
url = "https://storage.googleapis.com/google-code-archive-downloads/v2/code.google.com/ampliconnoise/AmpliconNoiseV1.29.tar.gz"
version("1.29", sha256="0bf946806d77ecaf0994ad8ebf9a5e98ad33c809f6def5c9340a16c367918167")
depends_on("mpi@2:")
depends_on("gsl")
patch("Fix-return-type.patch")
def setup_run_environment(self, env):
env.prepend_path("PATH", self.prefix.Scripts)
env.set("PYRO_LOOKUP_FILE", os.path.join(self.prefix, "Data", "LookUp_E123.dat"))
env.set("SEQ_LOOKUP_FILE", os.path.join(self.prefix, "Data", "Tran.dat"))
def install(self, spec, prefix):
make("install")
install_tree("bin", prefix.bin)
install_tree("Data", prefix.Data)
install_tree("FastaUnique", prefix.FastaUnique)
install_tree("FCluster", prefix.FCluster)
install_tree("NDist", prefix.NDist)
install_tree("Perseus", prefix.Perseus)
install_tree("PerseusD", prefix.PerseusD)
install_tree("PyroDist", prefix.PyroDist)
install_tree("PyroNoise", prefix.PyroNoise)
install_tree("PyroNoiseM", prefix.PyroNoiseM)
install_tree("Scripts", prefix.Scripts)
install_tree("SeqDist", prefix.SeqDist)
install_tree("SeqNoise", prefix.SeqNoise)
install_tree("SplitClusterClust", prefix.SplitClusterClust)
install_tree("SplitClusterEven", prefix.SplitClusterEven)
install_tree("Test", prefix.Test)
install_tree("TestFLX", prefix.TestFLX)
install_tree("TestTitanium", prefix.TestTitanium)
install_tree("TestTitaniumFast", prefix.TestTitaniumFast)
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