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authorAudrey Thoma <las_thoma15@iastate.edu>2017-10-10 13:09:31 -0500
committerscheibelp <scheibel1@llnl.gov>2017-10-10 11:09:31 -0700
commite3053d7425e10180a8a7d0521b89bdf710f87dc2 (patch)
tree35c73bbfee853aa322e7d35265834aff739e55e2
parentf2b49d8f6639dda9ab871743d8d6ffc47b44fb18 (diff)
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snap-korf: new package (#5589)
-rw-r--r--var/spack/repos/builtin/packages/snap-korf/package.py62
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
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+++ 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)