From 0dddb988696f3c90ea3c14c48346c265d744e2f2 Mon Sep 17 00:00:00 2001
From: Eric <erimar77@users.noreply.github.com>
Date: Sun, 6 May 2018 10:56:03 -0500
Subject: 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
---
.../repos/builtin/packages/metabat/package.py | 54 ++++++++++++++++++++++
1 file changed, 54 insertions(+)
create mode 100644 var/spack/repos/builtin/packages/metabat/package.py
(limited to 'var')
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')
--
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