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| -rw-r--r-- | var/spack/repos/builtin/packages/strelka/package.py | 88 |
1 files changed, 88 insertions, 0 deletions
diff --git a/var/spack/repos/builtin/packages/strelka/package.py b/var/spack/repos/builtin/packages/strelka/package.py new file mode 100644 index 0000000000..5c3da7c635 --- /dev/null +++ b/var/spack/repos/builtin/packages/strelka/package.py @@ -0,0 +1,88 @@ +############################################################################## +# Copyright (c) 2013-2017, 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/llnl/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 * + + +class Strelka(CMakePackage): + """Somatic and germline small variant caller for mapped sequencing + data.""" + + homepage = "https://github.com/Illumina/strelka" + url = "https://github.com/Illumina/strelka/releases/download/v2.8.2/strelka-2.8.2.release_src.tar.bz2" + + version('2.8.2', 'c48753997fcf2e4edac4e9854495721e') + + depends_on('python@2.4:') + depends_on('zlib') + depends_on('bzip2') + depends_on('cmake@2.8.5:') + depends_on('boost@1.56.0') + + @run_before('install') + def filter_sbang(self): + """Run before install so that the standard Spack sbang install hook + can fix up the path to the python binary. + """ + + match = '^#!/usr/bin/env python' + python = self.spec['python'].command + substitute = "#!{p}".format(p=python) + kwargs = {'ignore_absent': False, 'backup': False, 'string': False} + with working_dir('src'): + files = [ + 'config/validate/validateJsonModelFromSchema.py', + 'srcqc/run_cppcheck.py', + 'python/libexec/cat.py', + 'python/libexec/sortVcf.py', + 'python/libexec/extractSmallIndelCandidates.py', + 'python/libexec/configureStrelkaNoiseWorkflow.py', + 'python/libexec/configureSequenceErrorCountsWorkflow.py', + 'python/libexec/vcfCmdlineSwapper.py', + 'python/libexec/mergeChromDepth.py', + 'python/scoringModelTraining/germline/bin/evs_learn.py', + 'python/scoringModelTraining/germline/bin/parseAnnotatedTrainingVcf.py', # noqa: E501 + 'python/scoringModelTraining/germline/bin/filterTrainingVcf.py', # noqa: E501 + 'python/scoringModelTraining/germline/bin/evs_exportmodel.py', + 'python/scoringModelTraining/germline/bin/evs_qq.py', + 'python/scoringModelTraining/germline/bin/evs_pr.py', + 'python/scoringModelTraining/germline/bin/evs_evaluate.py', + 'python/scoringModelTraining/somatic/bin/evs_random_sample_tpfp.py', # noqa: E501 + 'python/scoringModelTraining/somatic/bin/evs_learn.py', + 'python/scoringModelTraining/somatic/bin/evs_random_split_csv.py', # noqa: E501 + 'python/scoringModelTraining/somatic/bin/vcf_to_feature_csv.py', # noqa: E501 + 'python/scoringModelTraining/somatic/bin/calc_features.py', + 'python/scoringModelTraining/somatic/bin/evs_exportmodel.py', + 'python/scoringModelTraining/somatic/bin/evs_pr.py', + 'python/scoringModelTraining/somatic/bin/evs_evaluate.py', + 'python/bin/configureStrelkaGermlineWorkflow.py', + 'python/bin/configureStrelkaSomaticWorkflow.py', + ] + filter_file(match, substitute, *files, **kwargs) + + with working_dir('spack-build/redist'): + files = [ + 'pyflow-1.1.18/src/pyflow.py', + ] + filter_file(match, substitute, *files, **kwargs) |