snap-korf: new package (#5589)

1 files changed, 62 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/snap-korf/package.py b/var/spack/repos/builtin/packages/snap-korf/package.py
new file mode 100644
index 0000000000..95191b1bd4
--- /dev/null
+++ b/var/spack/repos/builtin/packages/snap-korf/package.py
@@ -0,0 +1,62 @@
+##############################################################################
+# 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 *
+import glob
+
+
+class SnapKorf(MakefilePackage):
+    """SNAP is a general purpose gene finding program suitable for both
+       eukaryotic and prokaryotic genomes."""
+
+    homepage = "http://korflab.ucdavis.edu/software.html"
+    url      = "http://korflab.ucdavis.edu/Software/snap-2013-11-29.tar.gz"
+
+    version('2013-11-29', 'dfdf48e37cdb32af4eecd9201506b6e3')
+
+    depends_on('perl', type=('build', 'run'))
+    depends_on('boost')
+    depends_on('sqlite')
+    depends_on('sparsehash')
+
+    conflicts('%gcc@5:', when='@2013-11-29')
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.bin)
+
+        progs  = ['snap', 'fathom', 'forge', 'depend', 'exonpairs', 'hmm-info']
+        for p in progs:
+            install(p, prefix.bin)
+
+        files = glob.iglob('*.pl')
+        for file in files:
+            install(file, prefix.bin)
+
+        install_tree('Zoe', prefix.Zoe)
+        install_tree('HMM', prefix.HMM)
+        install_tree('DNA', prefix.DNA)
+
+    def setup_environment(self, spack_env, run_env):
+        run_env.set('ZOE', self.prefix)
+        run_env.prepend_path('PATH', self.prefix)