Add abyss package (#4555)

* abyss

* abyss: deleting attemped test from script

* abyss: adding new package abyss

* abyss: partially fixing mpi dependency issue

* abyss: added mpi provider conflicts

1 files changed, 54 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/abyss/package.py b/var/spack/repos/builtin/packages/abyss/package.py
new file mode 100644
index 0000000000..9f4a31a47e
--- /dev/null
+++ b/var/spack/repos/builtin/packages/abyss/package.py
@@ -0,0 +1,54 @@
+##############################################################################
+# 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 LICENSE file 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 Abyss(AutotoolsPackage):
+    """ABySS is a de novo, parallel, paired-end sequence assembler
+       that is designed for short reads. The single-processor version
+       is useful for assembling genomes up to 100 Mbases in size."""
+
+    homepage = "http://www.bcgsc.ca/platform/bioinfo/software/abyss"
+    url      = "http://www.bcgsc.ca/platform/bioinfo/software/abyss/releases/2.0.2/abyss-2.0.2.tar.gz"
+
+    version('2.0.2', '1623f55ad7f4586e80f6e74b1f27c798')
+
+    depends_on('mpi')
+    depends_on('boost@:1.50.0,1.53.0:')
+    depends_on('sparsehash')
+    depends_on('sqlite')
+
+    conflicts('^intel-mpi')
+    conflicts('^intel-parallel-studio+mpi')
+    conflicts('^mvapich2')
+    conflicts('^spectrum-mpi')
+
+    def configure_args(self):
+        args = ['--with-boost=%s' % self.spec['boost'].prefix,
+                '--with-sqlite=%s' % self.spec['sqlite'].prefix,
+                '--with-mpi=%s' % self.spec['mpi'].prefix]
+        if self.spec['mpi'].name == 'mpich':
+                args.append('--enable-mpich')
+        return args