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authorAudrey Thoma <las_thoma15@iastate.edu>2017-08-30 02:57:57 -0500
committerTodd Gamblin <tgamblin@llnl.gov>2017-08-30 00:57:57 -0700
commitde5111cd509b5a88dad20f71453b90678cb682fc (patch)
tree749276cc22f7ab8fe7b65fd8f2a17cf5514ac3b9 /var
parentc830eda0e6f8e773cdf2d8aeb9b400a307c834fe (diff)
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hapcut2: new package (#5238)
Diffstat (limited to 'var')
-rw-r--r--var/spack/repos/builtin/packages/hapcut2/package.py44
1 files changed, 44 insertions, 0 deletions
diff --git a/var/spack/repos/builtin/packages/hapcut2/package.py b/var/spack/repos/builtin/packages/hapcut2/package.py
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+++ b/var/spack/repos/builtin/packages/hapcut2/package.py
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+##############################################################################
+# 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 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 Hapcut2(MakefilePackage):
+ """HapCUT2 is a maximum-likelihood-based tool for assembling haplotypes
+ from DNA sequence reads, designed to 'just work' with excellent speed
+ and accuracy."""
+
+ homepage = "https://github.com/vibansal/HapCUT2"
+ url = "https://github.com/vibansal/HapCUT2"
+
+ version('2017-07-10', git='https://github.com/vibansal/HapCUT2.git',
+ commit='2966b94c2c2f97813b757d4999b7a6471df1160e', submodules=True)
+
+ def install(self, spec, prefix):
+ mkdirp(prefix.bin)
+ with working_dir('build'):
+ install('extractFOSMID', prefix.bin)
+ install('extractHAIRS', prefix.bin)
+ install('HAPCUT2', prefix.bin)