mira: new package (#6385)

var/spack/repos/builtin/packages/mira/package.py

@@ -0,0 +1,52 @@
+##############################################################################
+# Copyright (c) 2013-2017, 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/spack/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 Mira(AutotoolsPackage):
+    """MIRA is a multi-pass DNA sequence data assembler/mapper for whole genome
+       and EST/RNASeq projects."""
+
+    homepage = "http://sourceforge.net/projects/mira-assembler/"
+    url      = "https://downloads.sourceforge.net/project/mira-assembler/MIRA/stable/mira-4.0.2.tar.bz2"
+
+    version('4.0.2', '1921b426910653a34a6dbb37346f28ea')
+
+    depends_on('boost@1.46:')
+    depends_on('expat@2.0.1:')
+    depends_on('gperftools')
+
+    conflicts('%gcc@6:', when='@:4.0.2')
+
+    def patch(self):
+        with working_dir(join_path('src', 'progs')):
+            edit = FileFilter('quirks.C')
+            edit.filter('#include <boost/filesystem.hpp>',
+                        '#include <boost/filesystem.hpp>\n#include <iostream>')
+
+    def configure_args(self):
+        args = ['--with-boost=%s' % self.spec['boost'].prefix,
+                '--with-expat=%s' % self.spec['expat'].prefix]
+        return args