50 lines
2.0 KiB
Python
50 lines
2.0 KiB
Python
# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
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# Spack Project Developers. See the top-level COPYRIGHT file for details.
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#
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# SPDX-License-Identifier: (Apache-2.0 OR MIT)
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from spack import *
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class Pagit(Package):
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"""PAGIT addresses the need for software to generate high quality draft
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genomes."""
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homepage = "http://www.sanger.ac.uk/science/tools/pagit"
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url = "ftp://ftp.sanger.ac.uk/pub/resources/software/pagit/PAGIT.V1.01.64bit.tgz"
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version('1.01', '2c4e8512c8c02073146b50b328962e9d')
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depends_on('java', type=('build', 'run'))
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depends_on('perl', type=('build', 'run'))
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def url_for_version(self, version):
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url = 'ftp://ftp.sanger.ac.uk/pub/resources/software/pagit/PAGIT.V{0}.64bit.tgz'
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return url.format(version)
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def install(self, spec, prefix):
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with working_dir('PAGIT'):
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install_tree('ABACAS', prefix.ABACAS)
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install_tree('bin', prefix.bin)
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install_tree('ICORN', prefix.ICORN)
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install_tree('IMAGE', prefix.IMAGE)
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install_tree('lib', prefix.lib)
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install_tree('RATT', prefix.RATT)
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def setup_environment(self, spack_env, run_env):
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run_env.set('PAGIT_HOME', self.prefix)
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run_env.set('PILEUP_HOME', join_path(self.prefix.bin, 'pileup_v0.5'))
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run_env.set('ICORN_HOME', self.prefix.icorn)
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run_env.set('SNPOMATIC_HOME', self.prefix.bin)
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run_env.set('RATT_HOME', self.prefix.RATT)
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run_env.set('RATT_CONFIG', join_path(self.prefix.RATT, 'RATT_config'))
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run_env.prepend_path('PATH', join_path(self.prefix.bin, 'pileup_v0.5',
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'ssaha2'))
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run_env.prepend_path('PATH', join_path(self.prefix.bin,
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'pileup_v0.5'))
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run_env.prepend_path('PATH', self.prefix.IMAGE)
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run_env.prepend_path('PATH', self.prefix.ABACAS)
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run_env.prepend_path('PATH', self.prefix.ICORN)
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run_env.prepend_path('PATH', self.prefix.RATT)
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run_env.prepend_path('PERL5LIB', self.prefix.lib)
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