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##############################################################################
# Copyright (c) 2013-2018, 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 inspect
class Repeatmasker(Package):
"""RepeatMasker is a program that screens DNA sequences for interspersed
repeats and low complexity DNA sequences."""
homepage = "http://www.repeatmasker.org"
url = "http://www.repeatmasker.org/RepeatMasker-open-4-0-7.tar.gz"
version('4.0.7', '4dcbd7c88c5343e02d819f4b3e6527c6')
depends_on('perl', type=('build', 'run'))
depends_on('perl-text-soundex', type=('build', 'run'))
depends_on('hmmer')
depends_on('ncbi-rmblastn')
depends_on('trf')
def url_for_version(self, version):
url = 'http://www.repeatmasker.org/RepeatMasker-open-{0}.tar.gz'
return url.format(version.dashed)
def install(self, spec, prefix):
# Config questions consist of:
#
# <PRESS ENTER TO CONTINUE>
# Enter perl path
# Enter where repeatmasker is being configured from
# Enter trf path
# Add a Search Engine:
# 1. CrossMatch
# 2. RMBlast - NCBI Blast with RepeatMasker extensions
# 3. WUBlast/ABBlast (required by DupMasker)
# 4. HMMER3.1 & DFAM
# 5. Done
# Enter RMBlast path
# Do you want RMBlast to be your default search engine for
# Repeatmasker? (Y/N)
# Add a Search Engine: Done
config_answers = ['\n', '%s\n' % self.spec['perl'].command.path,
'%s\n' % self.stage.source_path,
'%s\n' % self.spec['trf'].prefix.bin.trf, '2\n',
'%s\n' % self.spec['ncbi-rmblastn'].prefix.bin,
'Y\n', '5\n']
config_answers_filename = 'spack-config.in'
with open(config_answers_filename, 'w') as f:
f.writelines(config_answers)
with open(config_answers_filename, 'r') as f:
inspect.getmodule(self).perl('configure', input=f)
install_tree('.', prefix.bin)
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