metabat: Create new package (#7991)

* metabat: Create new package

* fix Perl script shebangs and BOOST_ROOT environment

* add perl script fix function

* add perl dependency and fix positional argument for Python 2.6

1 files changed, 54 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/metabat/package.py b/var/spack/repos/builtin/packages/metabat/package.py
new file mode 100644
index 0000000000..3d00c2dbe6
--- /dev/null
+++ b/var/spack/repos/builtin/packages/metabat/package.py
@@ -0,0 +1,54 @@
+##############################################################################
+# Copyright (c) 2013-2018, 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 Metabat(SConsPackage):
+    """MetaBAT, an efficient tool for accurately reconstructing single
+    genomes from complex microbial communities."""
+
+    homepage = "https://bitbucket.org/berkeleylab/metabat"
+    url      = "https://bitbucket.org/berkeleylab/metabat/get/v2.12.1.tar.gz"
+
+    version('2.12.1', 'c032f47a8b24e58a5a9fefe52cb6e0f8')
+
+    depends_on('boost@1.55.0:', type=('build', 'run'))
+    depends_on('perl', type='run')
+
+    def setup_environment(self, spack_env, run_env):
+        spack_env.set('BOOST_ROOT', self.spec['boost'].prefix)
+
+    def install_args(self, spec, prefix):
+        return ["PREFIX={0}".format(prefix)]
+
+    @run_after('build')
+    def fix_perl_scripts(self):
+        filter_file(r'#!/usr/bin/perl',
+                    '#!/usr/bin/env perl',
+                    'aggregateBinDepths.pl')
+
+        filter_file(r'#!/usr/bin/perl',
+                    '#!/usr/bin/env perl',
+                    'aggregateContigOverlapsByBin.pl')