Package ampliconnoise (#4676)

* ampliconnoise: new package

* ampliconnoise: fixed installation

* ampliconnoise: fixing install again

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)