New package augustus (#4586)

* augustus: adding augustus

* augustus: fixing flake8 things

* augustus: simplifying verbose

1 files changed, 70 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/augustus/package.py b/var/spack/repos/builtin/packages/augustus/package.py
new file mode 100644
index 0000000000..ccaa2f1e70
--- /dev/null
+++ b/var/spack/repos/builtin/packages/augustus/package.py
@@ -0,0 +1,70 @@
+##############################################################################
+# 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 LICENSE file 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 Augustus(MakefilePackage):
+    """AUGUSTUS is a program that predicts genes in eukaryotic
+       genomic sequences"""
+
+    homepage = "http://bioinf.uni-greifswald.de/augustus/"
+    url      = "http://bioinf.uni-greifswald.de/augustus/binaries/augustus-3.2.3.tar.gz"
+
+    version('3.2.3', 'b8c47ea8d0c45aa7bb9a82626c8ff830')
+
+    depends_on('bamtools')
+    depends_on('gsl')
+    depends_on('boost')
+    depends_on('zlib')
+
+    def edit(self, spec, prefix):
+        with working_dir(join_path('auxprogs', 'filterBam', 'src')):
+            makefile = FileFilter('Makefile')
+            makefile.filter('BAMTOOLS = .*', 'BAMTOOLS = %s' % self.spec[
+                            'bamtools'].prefix)
+            makefile.filter('INCLUDES = *',
+                            'INCLUDES = -I$(BAMTOOLS)/include/bamtools ')
+            makefile.filter('LIBS = -lbamtools -lz',
+                            'LIBS = $(BAMTOOLS)/lib/bamtools'
+                            '/libbamtools.a -lz')
+        with working_dir(join_path('auxprogs', 'bam2hints')):
+            makefile = FileFilter('Makefile')
+            makefile.filter('# Variable definition',
+                            'BAMTOOLS = %s' % self.spec['bamtools'].prefix)
+            makefile.filter('INCLUDES = /usr/include/bamtools',
+                            'INCLUDES = $(BAMTOOLS)/include/bamtools')
+            makefile.filter('LIBS = -lbamtools -lz',
+                            'LIBS = $(BAMTOOLS)/lib/bamtools'
+                            '/libbamtools.a -lz')
+
+    def install(self, spec, prefix):
+        install_tree('bin', join_path(self.spec.prefix, 'bin'))
+        install_tree('config', join_path(self.spec.prefix, 'config'))
+        install_tree('scripts', join_path(self.spec.prefix, 'scripts'))
+
+    def setup_environment(self, spack_env, run_env):
+        run_env.set('AUGUSTUS_CONFIG_PATH', join_path(
+            self.prefix, 'config'))
+        run_env.prepend_path('PATH', join_path(self.prefix, 'scripts'))