orthomcl: new package (#5345)

Add orthocml package and fix mariadb url

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

@@ -33,11 +33,11 @@ class Mariadb(CMakePackage):
     tools make it very versatile for a wide variety of use cases."""
 
     homepage = "https://mariadb.org/about/"
-    url      = "https://downloads.mariadb.org/f/mariadb-10.1.23/source/mariadb-10.1.23.tar.gz"
+    url      = "http://ftp.hosteurope.de/mirror/archive.mariadb.org/mariadb-10.2.8/source/mariadb-10.2.8.tar.gz"
 
+    version('10.2.8', 'f93cbd5bfde3c0d082994764ff7db580')
     version('10.1.23', '1a7392cc05c7c249acd4495022719ca8')
     version('5.5.56', '8bc7772fea3e11b0bc1a09d2278e2e32')
-    # old versions, do not fetch under given url anymore
     version('10.1.14', '294925531e0fd2f0461e3894496a5adc')
     version('5.5.49', '67b5a499a5f158b2a586e6e3bfb4f304')
 

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

@@ -0,0 +1,49 @@
+##############################################################################
+# 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/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 Orthomcl(Package):
+    """OrthoMCL is a genome-scale algorithm for grouping orthologous protein
+       sequences."""
+
+    homepage = "http://orthomcl.org/orthomcl/"
+    url      = "http://orthomcl.org/common/downloads/software/v2.0/orthomclSoftware-v2.0.9.tar.gz"
+
+    version('2.0.9', '2e0202ed4e36a753752c3567edb9bba9')
+
+    depends_on('perl', type=('build', 'run'))
+    depends_on('blast-plus')
+    depends_on('mcl')
+    depends_on('mariadb')
+
+    def install(self, spec, prefix):
+        install_tree('bin', prefix.bin)
+        install_tree('config', prefix.config)
+        install_tree('doc', prefix.doc)
+        install_tree('lib', prefix.lib)
+
+    def setup_environment(self, spack_env, run_env):
+        run_env.prepend_path('PERL5LIB', self.prefix.lib)