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| -rw-r--r-- | var/spack/repos/builtin/packages/ampliconnoise/package.py | 67 |
1 files changed, 67 insertions, 0 deletions
diff --git a/var/spack/repos/builtin/packages/ampliconnoise/package.py b/var/spack/repos/builtin/packages/ampliconnoise/package.py new file mode 100644 index 0000000000..7051ae0008 --- /dev/null +++ b/var/spack/repos/builtin/packages/ampliconnoise/package.py @@ -0,0 +1,67 @@ +############################################################################## +# 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) |