53 lines
2.2 KiB
Python
53 lines
2.2 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 Breakdancer(CMakePackage):
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"""BreakDancer-1.3.6, released under GPLv3, is a perl/Cpp package that
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provides genome-wide detection of structural variants from next generation
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paired-end sequencing reads. It includes two complementary programs.
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BreakDancerMax predicts five types of structural variants: insertions,
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deletions, inversions, inter- and intra-chromosomal translocations from
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next-generation short paired-end sequencing reads using read pairs that are
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mapped with unexpected separation distances or orientation.
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BreakDancerMini focuses on detecting small indels (usually between 10bp and
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100bp) using normally mapped read pairs.."""
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homepage = "http://gmt.genome.wustl.edu/packages/breakdancer"
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url = "https://github.com/genome/breakdancer/archive/v1.4.5.tar.gz"
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version('1.4.5', sha256='5d74f3a90f5c69026ebb4cf4cb9ccc51ec8dd49ac7a88595a1efabd5a73e92b6')
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version('master', submodules='true',
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git='https://github.com/genome/breakdancer.git', preferred=True)
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phases = ['edit', 'cmake', 'build', 'install']
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depends_on('zlib')
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depends_on('perl-statistics-descriptive', type='run')
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depends_on('perl-math-cdf', type='run')
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depends_on('perl-gd-graph', type='run')
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depends_on('perl-gdgraph-histogram', type='run')
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depends_on('perl-list-moreutils', type='run')
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depends_on('perl-exporter-tiny', type='run')
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# TODO: remove git submodules, and depend on boost & samtools
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parallel = False
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def setup_environment(self, spack_env, run_env):
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# get the perl tools in the path
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run_env.prepend_path('PATH', self.prefix.lib)
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def edit(self, spec, prefix):
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# perl tools end up in a silly lib subdirectory, fixing that
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filter_file(r'set\(SUPPORT_LIBDIR lib\/breakdancer-max\$ \
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\{EXE_VERSION_SUFFIX\}\)',
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'set(SUPPORT_LIBDIR lib)',
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join_path(self.stage.source_path,
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'perl', 'CMakeLists.txt'))
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