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guidance: new package (#6079)

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* guidance: new package

* not really fixed yet

* adding loop

* fixing url

* dang typos
This commit is contained in:
Audrey Thoma 2017-11-08 15:07:13 -06:00 committed by Christoph Junghans
parent dd3a6d7f18
commit 877bee3cb5
1 changed files with 66 additions and 0 deletions
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var/spack/repos/builtin/packages/guidance/package.py Normal file
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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/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)