diff options
Diffstat (limited to 'var')
| -rw-r--r-- | var/spack/repos/builtin/packages/strelka/package.py | 60 |
1 files changed, 13 insertions, 47 deletions
diff --git a/var/spack/repos/builtin/packages/strelka/package.py b/var/spack/repos/builtin/packages/strelka/package.py index e86d90d878..d1d2e0d9ec 100644 --- a/var/spack/repos/builtin/packages/strelka/package.py +++ b/var/spack/repos/builtin/packages/strelka/package.py @@ -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) |