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Update strelka (#19565)

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* Update package.py

Remove breaking patch.

Patching the shebang is useless is the dependencies are properly loaded before execution. Furthermore, the long paths which can be generated when installing with Spack can exceed the maximum length of the shebang.

* Add newer versions of strelka.
This commit is contained in:
dunatotatos 2020-10-28 16:58:30 +01:00 committed by GitHub
parent 1dd7370885
commit f028079564
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GPG Key ID: 4AEE18F83AFDEB23
1 changed files with 13 additions and 47 deletions
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60
var/spack/repos/builtin/packages/strelka/package.py
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@ -13,6 +13,19 @@ class Strelka(CMakePackage):
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('2.9.10', sha256='45e78efec6e5272697f1d0a95851c7ae0d623dc8f93846e11fe37f15da9f1e30')
version('2.9.9', sha256='547b42ab983ba38a6459d47e8546daa6d571f370933542f02f3f3bd9abd13c16')
version('2.9.8', sha256='dc12b894e1267a63f7049bc01402b284db1681c82fb2cac313324a6530cbc4ad')
version('2.9.7', sha256='9b0db7cc32662488ea53931e1afccff3e7967cd3b492cc93e66a8115a1f4d016')
version('2.9.6', sha256='db6fe97add75309954bb46f9c53e1c722d8a8d66adc976ff7e2e9788b7ff97fa')
version('2.9.5', sha256='b3d70129508226280f4de9c328f3cd751e4cedba4383b0264a16ac37f73b1412')
version('2.9.4', sha256='d06088bb2b033cfcda7263fe8fcf915cba10c77df963f116f64a57cd2682803f')
version('2.9.3', sha256='9f2cd17b5326f09c499fb01d32d1bb61dec9a97c70199f685824e89bfcad2dee')
version('2.9.2', sha256='47642c3138e126efaab485a40a9a954abfed34f8c88b107a46dbd64e3f1778a5')
version('2.9.1', sha256='963e1935389d8777bcdfe77f6126a34a0f8ea5cc27a280e41ba67e9df88cf990')
version('2.9.0', sha256='25b4dbd270f541bc6a172d12448c209586e9f00e86f56cfce98d1d5612bb4fb8')
version('2.8.4', sha256='523fb89e7ba7717a61548fcd45b0ccd5c850a8f2b034ab1cf34ec74efb7260c2')
version('2.8.3', sha256='4f6f8f433a3e1d7a59243bd75bc73dcfb309c1dacc79fe56fafd0ad96e856415')
version('2.8.2', sha256='27415f7c14f92e0a6b80416283a0707daed121b8a3854196872981d132f1496b')
depends_on('python@2.4:2.7')
@ -20,50 +33,3 @@ class Strelka(CMakePackage):
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)