meraculous: new package (#6292)

* meraculous: new package

* adding gcc version conflict

* Update package.py

* Update package.py

2 files changed, 84 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/meraculous/package.py b/var/spack/repos/builtin/packages/meraculous/package.py
new file mode 100644
index 0000000000..51d3943943
--- /dev/null
+++ b/var/spack/repos/builtin/packages/meraculous/package.py
@@ -0,0 +1,50 @@
+##############################################################################
+# 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 Meraculous(CMakePackage):
+    """Meraculous is a while genome assembler for Next Generation Sequencing
+       data geared for large genomes."""
+
+    homepage = "http://jgi.doe.gov/data-and-tools/meraculous/"
+    url      = "https://downloads.sourceforge.net/project/meraculous20/Meraculous-v2.2.4.tar.gz"
+
+    version('2.2.4', '349feb6cb178643a46e4b092c87bad3a')
+
+    depends_on('perl', type=('build', 'run'))
+    depends_on('boost@1.5.0:')
+    depends_on('gnuplot@3.7:')
+    depends_on('perl-log-log4perl', type=('build', 'run'))
+
+    conflicts('%gcc@6.0.0:', when='@2.2.4')
+
+    def patch(self):
+        edit = FileFilter('CMakeLists.txt')
+        edit.filter("-static-libstdc\+\+", "")
+
+    def setup_environment(self, spack_env, run_env):
+        run_env.set('MERACULOUS_ROOT', self.prefix)
+        run_env.prepend_path('PERL5LIB', self.prefix.lib)
diff --git a/var/spack/repos/builtin/packages/perl-log-log4perl/package.py b/var/spack/repos/builtin/packages/perl-log-log4perl/package.py
new file mode 100644
index 0000000000..6a0d182d2f
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-log-log4perl/package.py
@@ -0,0 +1,34 @@
+##############################################################################
+# 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 PerlLogLog4perl(PerlPackage):
+    """Log4j implementation for Perl"""
+
+    homepage = "http://search.cpan.org/~mschilli/Log-Log4perl-1.44/lib/Log/Log4perl.pm"
+    url      = "https://github.com/mschilli/log4perl/archive/rel_146.tar.gz"
+
+    version('146', '500abbd978ed326cfe5367dc4f9f3be2')