cdhit: new package (#5085)

1 files changed, 49 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/cdhit/package.py b/var/spack/repos/builtin/packages/cdhit/package.py
new file mode 100644
index 0000000000..8651466ef5
--- /dev/null
+++ b/var/spack/repos/builtin/packages/cdhit/package.py
@@ -0,0 +1,49 @@
+##############################################################################
+# 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 Cdhit(MakefilePackage):
+    """CD-HIT is a very widely used program for clustering and comparing
+       protein or nucleotide sequences."""
+
+    homepage = "http://cd-hit.org/"
+    url      = "https://github.com/weizhongli/cdhit/archive/V4.6.8.tar.gz"
+
+    version('4.6.8', 'bdd73ec0cceab6653aab7b31b57c5a8b')
+
+    variant('openmp', default=True, description='Compile with multi-threading support')
+
+    depends_on('perl', type=('build', 'run'))
+
+    def build(self, spec, prefix):
+        mkdirp(prefix.bin)
+        if '~openmp' in spec:
+            make('openmp=no')
+        else:
+            make()
+
+    def setup_environment(self, spack_env, run_env):
+        spack_env.set('PREFIX', prefix.bin)