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# 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)
import os.path
class Ampliconnoise(MakefilePackage):
"""AmpliconNoise is a collection of programs for the removal of noise
from 454 sequenced PCR amplicons."""
homepage = "https://code.google.com/archive/p/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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