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Package ampliconnoise (#4676)

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* ampliconnoise: new package

* ampliconnoise: fixed installation

* ampliconnoise: fixing install again
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Audrey Thoma 2017-07-05 13:30:40 -05:00 committed by Adam J. Stewart
parent f403117f71
commit 09681f721d
1 changed files with 67 additions and 0 deletions
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##############################################################################
# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-647188
#
# For details, see https://github.com/llnl/spack
# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License (as
# published by the Free Software Foundation) version 2.1, February 1999.
#
# This program is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
# conditions of the GNU Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
# License along with this program; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
##############################################################################
from spack import *
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', 'd6723e6f9cc71d7eb6f1a65ba4643aac')
depends_on('mpi@2:')
depends_on('gsl')
def setup_environment(self, spack_env, run_env):
run_env.prepend_path('PATH', self.prefix.Scripts)
run_env.set('PYRO_LOOKUP_FILE', join_path(self.prefix, 'Data',
'LookUp_E123.dat'))
run_env.set('SEQ_LOOKUP_FILE', join_path(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)