70 lines
3.3 KiB
Python
70 lines
3.3 KiB
Python
# Copyright 2013-2020 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 Strelka(CMakePackage):
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"""Somatic and germline small variant caller for mapped sequencing
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data."""
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homepage = "https://github.com/Illumina/strelka"
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url = "https://github.com/Illumina/strelka/releases/download/v2.8.2/strelka-2.8.2.release_src.tar.bz2"
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version('2.8.2', sha256='27415f7c14f92e0a6b80416283a0707daed121b8a3854196872981d132f1496b')
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depends_on('python@2.4:2.7')
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depends_on('zlib')
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depends_on('bzip2')
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depends_on('cmake@2.8.5:')
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depends_on('boost@1.56.0:')
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@run_before('install')
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def filter_sbang(self):
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"""Run before install so that the standard Spack sbang install hook
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can fix up the path to the python binary.
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"""
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match = '^#!/usr/bin/env python'
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python = self.spec['python'].command
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substitute = "#!{p}".format(p=python)
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kwargs = {'ignore_absent': False, 'backup': False, 'string': False}
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with working_dir('src'):
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files = [
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'config/validate/validateJsonModelFromSchema.py',
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'srcqc/run_cppcheck.py',
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'python/libexec/cat.py',
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'python/libexec/sortVcf.py',
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'python/libexec/extractSmallIndelCandidates.py',
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'python/libexec/configureStrelkaNoiseWorkflow.py',
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'python/libexec/configureSequenceErrorCountsWorkflow.py',
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'python/libexec/vcfCmdlineSwapper.py',
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'python/libexec/mergeChromDepth.py',
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'python/scoringModelTraining/germline/bin/evs_learn.py',
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'python/scoringModelTraining/germline/bin/parseAnnotatedTrainingVcf.py', # noqa: E501
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'python/scoringModelTraining/germline/bin/filterTrainingVcf.py', # noqa: E501
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'python/scoringModelTraining/germline/bin/evs_exportmodel.py',
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'python/scoringModelTraining/germline/bin/evs_qq.py',
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'python/scoringModelTraining/germline/bin/evs_pr.py',
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'python/scoringModelTraining/germline/bin/evs_evaluate.py',
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'python/scoringModelTraining/somatic/bin/evs_random_sample_tpfp.py', # noqa: E501
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'python/scoringModelTraining/somatic/bin/evs_learn.py',
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'python/scoringModelTraining/somatic/bin/evs_random_split_csv.py', # noqa: E501
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'python/scoringModelTraining/somatic/bin/vcf_to_feature_csv.py', # noqa: E501
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'python/scoringModelTraining/somatic/bin/calc_features.py',
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'python/scoringModelTraining/somatic/bin/evs_exportmodel.py',
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'python/scoringModelTraining/somatic/bin/evs_pr.py',
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'python/scoringModelTraining/somatic/bin/evs_evaluate.py',
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'python/bin/configureStrelkaGermlineWorkflow.py',
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'python/bin/configureStrelkaSomaticWorkflow.py',
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]
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filter_file(match, substitute, *files, **kwargs)
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with working_dir('spack-build/redist'):
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files = [
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'pyflow-1.1.18/src/pyflow.py',
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]
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filter_file(match, substitute, *files, **kwargs)
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