Update strelka (#19565)

* 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.

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)