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authorAudrey Thoma <las_thoma15@iastate.edu>2017-11-08 15:07:13 -0600
committerChristoph Junghans <christoph.junghans@gmail.com>2017-11-08 14:07:13 -0700
commit877bee3cb5f506130f99c81b66a238579a30b87f (patch)
treee793d46177b06a7260e0fde3e18b62fcec94c35c
parentdd3a6d7f18e784234e602a6aca876f9f70dfa997 (diff)
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guidance: new package (#6079)
* guidance: new package * not really fixed yet * adding loop * fixing url * dang typos
-rw-r--r--var/spack/repos/builtin/packages/guidance/package.py66
1 files changed, 66 insertions, 0 deletions
diff --git a/var/spack/repos/builtin/packages/guidance/package.py b/var/spack/repos/builtin/packages/guidance/package.py
new file mode 100644
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+++ b/var/spack/repos/builtin/packages/guidance/package.py
@@ -0,0 +1,66 @@
+##############################################################################
+# 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/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 *
+import glob
+
+
+class Guidance(MakefilePackage):
+ """Guidance: Accurate detection of unreliable alignment regions accounting
+ for the uncertainty of multiple parameters."""
+
+ homepage = "http://guidance.tau.ac.il/ver2/"
+ url = "http://guidance.tau.ac.il/ver2/guidance.v2.02.tar.gz"
+
+ version('2.02', 'aa6ae2168e8e0237ee56bc2ac81202cf')
+
+ depends_on('perl', type=('build', 'run'))
+ depends_on('perl-bio-perl', type=('build', 'run'))
+ depends_on('ruby')
+ depends_on('prank')
+ depends_on('clustalw')
+ depends_on('mafft')
+ depends_on('muscle')
+
+ conflicts('%gcc@6.2.0:')
+
+ def edit(self, spec, prefix):
+ for dir in 'Guidance', 'Selecton', 'bioSequence_scripts_and_constants':
+ with working_dir(join_path('www', dir)):
+ files = glob.iglob('*.pl')
+ for file in files:
+ perl = FileFilter(file)
+ perl.filter('#!/usr/bin/perl -w', '#!/usr/bin/env perl')
+
+ def install(self, spac, prefix):
+ mkdir(prefix.bin)
+ install_tree('libs', prefix.bin.libs)
+ install_tree('programs', prefix.bin.programs)
+ install_tree('www', prefix.bin.www)
+ with working_dir(join_path('www', 'Guidance')): # copy without suffix
+ install('guidance.pl', join_path(prefix.bin.www.Guidance,
+ 'guidance'))
+
+ def setup_environment(self, spack_env, run_env):
+ run_env.prepend_path('PATH', prefix.bin.www.Guidance)