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-rw-r--r--var/spack/repos/builtin/packages/ampliconnoise/package.py67
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
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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)