toil 8.1.0b1__py3-none-any.whl → 8.2.0__py3-none-any.whl

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (254) hide show
  1. toil/__init__.py +0 -35
  2. toil/batchSystems/abstractBatchSystem.py +1 -1
  3. toil/batchSystems/abstractGridEngineBatchSystem.py +1 -1
  4. toil/batchSystems/awsBatch.py +1 -1
  5. toil/batchSystems/cleanup_support.py +1 -1
  6. toil/batchSystems/kubernetes.py +53 -7
  7. toil/batchSystems/local_support.py +1 -1
  8. toil/batchSystems/mesos/batchSystem.py +13 -8
  9. toil/batchSystems/mesos/test/__init__.py +3 -2
  10. toil/batchSystems/singleMachine.py +1 -1
  11. toil/batchSystems/slurm.py +27 -26
  12. toil/bus.py +5 -3
  13. toil/common.py +39 -11
  14. toil/cwl/cwltoil.py +1 -1
  15. toil/job.py +64 -49
  16. toil/jobStores/abstractJobStore.py +24 -3
  17. toil/jobStores/fileJobStore.py +25 -1
  18. toil/jobStores/googleJobStore.py +104 -30
  19. toil/leader.py +9 -0
  20. toil/lib/accelerators.py +3 -1
  21. toil/lib/aws/utils.py.orig +504 -0
  22. toil/lib/bioio.py +1 -1
  23. toil/lib/docker.py +252 -91
  24. toil/lib/dockstore.py +11 -3
  25. toil/lib/exceptions.py +5 -3
  26. toil/lib/history.py +87 -13
  27. toil/lib/history_submission.py +23 -9
  28. toil/lib/io.py +34 -22
  29. toil/lib/misc.py +7 -1
  30. toil/lib/resources.py +2 -1
  31. toil/lib/threading.py +11 -10
  32. toil/options/common.py +8 -0
  33. toil/options/wdl.py +11 -0
  34. toil/server/api_spec/LICENSE +201 -0
  35. toil/server/api_spec/README.rst +5 -0
  36. toil/server/cli/wes_cwl_runner.py +2 -1
  37. toil/test/__init__.py +275 -115
  38. toil/test/batchSystems/batchSystemTest.py +227 -205
  39. toil/test/batchSystems/test_slurm.py +27 -0
  40. toil/test/cactus/pestis.tar.gz +0 -0
  41. toil/test/conftest.py +7 -0
  42. toil/test/cwl/2.fasta +11 -0
  43. toil/test/cwl/2.fastq +12 -0
  44. toil/test/cwl/conftest.py +1 -1
  45. toil/test/cwl/cwlTest.py +999 -867
  46. toil/test/cwl/directory/directory/file.txt +15 -0
  47. toil/test/cwl/download_directory_file.json +4 -0
  48. toil/test/cwl/download_directory_s3.json +4 -0
  49. toil/test/cwl/download_file.json +6 -0
  50. toil/test/cwl/download_http.json +6 -0
  51. toil/test/cwl/download_https.json +6 -0
  52. toil/test/cwl/download_s3.json +6 -0
  53. toil/test/cwl/download_subdirectory_file.json +5 -0
  54. toil/test/cwl/download_subdirectory_s3.json +5 -0
  55. toil/test/cwl/empty.json +1 -0
  56. toil/test/cwl/mock_mpi/fake_mpi.yml +8 -0
  57. toil/test/cwl/mock_mpi/fake_mpi_run.py +42 -0
  58. toil/test/cwl/optional-file-exists.json +6 -0
  59. toil/test/cwl/optional-file-missing.json +6 -0
  60. toil/test/cwl/preemptible_expression.json +1 -0
  61. toil/test/cwl/revsort-job-missing.json +6 -0
  62. toil/test/cwl/revsort-job.json +6 -0
  63. toil/test/cwl/s3_secondary_file.json +16 -0
  64. toil/test/cwl/seqtk_seq_job.json +6 -0
  65. toil/test/cwl/stream.json +6 -0
  66. toil/test/cwl/test_filename_conflict_resolution.ms/table.dat +0 -0
  67. toil/test/cwl/test_filename_conflict_resolution.ms/table.f0 +0 -0
  68. toil/test/cwl/test_filename_conflict_resolution.ms/table.f1 +0 -0
  69. toil/test/cwl/test_filename_conflict_resolution.ms/table.f1i +0 -0
  70. toil/test/cwl/test_filename_conflict_resolution.ms/table.f2 +0 -0
  71. toil/test/cwl/test_filename_conflict_resolution.ms/table.f2_TSM0 +0 -0
  72. toil/test/cwl/test_filename_conflict_resolution.ms/table.f3 +0 -0
  73. toil/test/cwl/test_filename_conflict_resolution.ms/table.f3_TSM0 +0 -0
  74. toil/test/cwl/test_filename_conflict_resolution.ms/table.f4 +0 -0
  75. toil/test/cwl/test_filename_conflict_resolution.ms/table.f4_TSM0 +0 -0
  76. toil/test/cwl/test_filename_conflict_resolution.ms/table.f5 +0 -0
  77. toil/test/cwl/test_filename_conflict_resolution.ms/table.info +0 -0
  78. toil/test/cwl/test_filename_conflict_resolution.ms/table.lock +0 -0
  79. toil/test/cwl/whale.txt +16 -0
  80. toil/test/docs/scripts/example_alwaysfail.py +38 -0
  81. toil/test/docs/scripts/example_alwaysfail_with_files.wdl +33 -0
  82. toil/test/docs/scripts/example_cachingbenchmark.py +117 -0
  83. toil/test/docs/scripts/stagingExampleFiles/in.txt +1 -0
  84. toil/test/docs/scripts/stagingExampleFiles/out.txt +2 -0
  85. toil/test/docs/scripts/tutorial_arguments.py +23 -0
  86. toil/test/docs/scripts/tutorial_debugging.patch +12 -0
  87. toil/test/docs/scripts/tutorial_debugging_hangs.wdl +126 -0
  88. toil/test/docs/scripts/tutorial_debugging_works.wdl +129 -0
  89. toil/test/docs/scripts/tutorial_docker.py +20 -0
  90. toil/test/docs/scripts/tutorial_dynamic.py +24 -0
  91. toil/test/docs/scripts/tutorial_encapsulation.py +28 -0
  92. toil/test/docs/scripts/tutorial_encapsulation2.py +29 -0
  93. toil/test/docs/scripts/tutorial_helloworld.py +15 -0
  94. toil/test/docs/scripts/tutorial_invokeworkflow.py +27 -0
  95. toil/test/docs/scripts/tutorial_invokeworkflow2.py +30 -0
  96. toil/test/docs/scripts/tutorial_jobfunctions.py +22 -0
  97. toil/test/docs/scripts/tutorial_managing.py +29 -0
  98. toil/test/docs/scripts/tutorial_managing2.py +56 -0
  99. toil/test/docs/scripts/tutorial_multiplejobs.py +25 -0
  100. toil/test/docs/scripts/tutorial_multiplejobs2.py +21 -0
  101. toil/test/docs/scripts/tutorial_multiplejobs3.py +22 -0
  102. toil/test/docs/scripts/tutorial_promises.py +25 -0
  103. toil/test/docs/scripts/tutorial_promises2.py +30 -0
  104. toil/test/docs/scripts/tutorial_quickstart.py +22 -0
  105. toil/test/docs/scripts/tutorial_requirements.py +44 -0
  106. toil/test/docs/scripts/tutorial_services.py +45 -0
  107. toil/test/docs/scripts/tutorial_staging.py +45 -0
  108. toil/test/docs/scripts/tutorial_stats.py +64 -0
  109. toil/test/lib/aws/test_iam.py +3 -1
  110. toil/test/lib/dockerTest.py +205 -122
  111. toil/test/lib/test_history.py +101 -77
  112. toil/test/provisioners/aws/awsProvisionerTest.py +12 -9
  113. toil/test/provisioners/clusterTest.py +4 -4
  114. toil/test/provisioners/gceProvisionerTest.py +16 -14
  115. toil/test/sort/sort.py +4 -1
  116. toil/test/src/busTest.py +17 -17
  117. toil/test/src/deferredFunctionTest.py +145 -132
  118. toil/test/src/importExportFileTest.py +71 -63
  119. toil/test/src/jobEncapsulationTest.py +27 -28
  120. toil/test/src/jobServiceTest.py +149 -133
  121. toil/test/src/jobTest.py +219 -211
  122. toil/test/src/miscTests.py +66 -60
  123. toil/test/src/promisedRequirementTest.py +163 -169
  124. toil/test/src/regularLogTest.py +24 -24
  125. toil/test/src/resourceTest.py +82 -76
  126. toil/test/src/restartDAGTest.py +51 -47
  127. toil/test/src/resumabilityTest.py +24 -19
  128. toil/test/src/retainTempDirTest.py +60 -57
  129. toil/test/src/systemTest.py +17 -13
  130. toil/test/src/threadingTest.py +29 -32
  131. toil/test/utils/ABCWorkflowDebug/B_file.txt +1 -0
  132. toil/test/utils/ABCWorkflowDebug/debugWorkflow.py +204 -0
  133. toil/test/utils/ABCWorkflowDebug/mkFile.py +16 -0
  134. toil/test/utils/ABCWorkflowDebug/sleep.cwl +12 -0
  135. toil/test/utils/ABCWorkflowDebug/sleep.yaml +1 -0
  136. toil/test/utils/toilDebugTest.py +117 -102
  137. toil/test/utils/toilKillTest.py +54 -53
  138. toil/test/utils/utilsTest.py +303 -229
  139. toil/test/wdl/lint_error.wdl +9 -0
  140. toil/test/wdl/md5sum/empty_file.json +1 -0
  141. toil/test/wdl/md5sum/md5sum-gs.json +1 -0
  142. toil/test/wdl/md5sum/md5sum.1.0.wdl +32 -0
  143. toil/test/wdl/md5sum/md5sum.input +1 -0
  144. toil/test/wdl/md5sum/md5sum.json +1 -0
  145. toil/test/wdl/md5sum/md5sum.wdl +25 -0
  146. toil/test/wdl/miniwdl_self_test/inputs-namespaced.json +1 -0
  147. toil/test/wdl/miniwdl_self_test/inputs.json +1 -0
  148. toil/test/wdl/miniwdl_self_test/self_test.wdl +40 -0
  149. toil/test/wdl/standard_library/as_map.json +16 -0
  150. toil/test/wdl/standard_library/as_map_as_input.wdl +23 -0
  151. toil/test/wdl/standard_library/as_pairs.json +7 -0
  152. toil/test/wdl/standard_library/as_pairs_as_input.wdl +23 -0
  153. toil/test/wdl/standard_library/ceil.json +3 -0
  154. toil/test/wdl/standard_library/ceil_as_command.wdl +16 -0
  155. toil/test/wdl/standard_library/ceil_as_input.wdl +16 -0
  156. toil/test/wdl/standard_library/collect_by_key.json +1 -0
  157. toil/test/wdl/standard_library/collect_by_key_as_input.wdl +23 -0
  158. toil/test/wdl/standard_library/cross.json +11 -0
  159. toil/test/wdl/standard_library/cross_as_input.wdl +19 -0
  160. toil/test/wdl/standard_library/flatten.json +7 -0
  161. toil/test/wdl/standard_library/flatten_as_input.wdl +18 -0
  162. toil/test/wdl/standard_library/floor.json +3 -0
  163. toil/test/wdl/standard_library/floor_as_command.wdl +16 -0
  164. toil/test/wdl/standard_library/floor_as_input.wdl +16 -0
  165. toil/test/wdl/standard_library/keys.json +8 -0
  166. toil/test/wdl/standard_library/keys_as_input.wdl +24 -0
  167. toil/test/wdl/standard_library/length.json +7 -0
  168. toil/test/wdl/standard_library/length_as_input.wdl +16 -0
  169. toil/test/wdl/standard_library/length_as_input_with_map.json +7 -0
  170. toil/test/wdl/standard_library/length_as_input_with_map.wdl +17 -0
  171. toil/test/wdl/standard_library/length_invalid.json +3 -0
  172. toil/test/wdl/standard_library/range.json +3 -0
  173. toil/test/wdl/standard_library/range_0.json +3 -0
  174. toil/test/wdl/standard_library/range_as_input.wdl +17 -0
  175. toil/test/wdl/standard_library/range_invalid.json +3 -0
  176. toil/test/wdl/standard_library/read_boolean.json +3 -0
  177. toil/test/wdl/standard_library/read_boolean_as_command.wdl +17 -0
  178. toil/test/wdl/standard_library/read_float.json +3 -0
  179. toil/test/wdl/standard_library/read_float_as_command.wdl +17 -0
  180. toil/test/wdl/standard_library/read_int.json +3 -0
  181. toil/test/wdl/standard_library/read_int_as_command.wdl +17 -0
  182. toil/test/wdl/standard_library/read_json.json +3 -0
  183. toil/test/wdl/standard_library/read_json_as_output.wdl +31 -0
  184. toil/test/wdl/standard_library/read_lines.json +3 -0
  185. toil/test/wdl/standard_library/read_lines_as_output.wdl +31 -0
  186. toil/test/wdl/standard_library/read_map.json +3 -0
  187. toil/test/wdl/standard_library/read_map_as_output.wdl +31 -0
  188. toil/test/wdl/standard_library/read_string.json +3 -0
  189. toil/test/wdl/standard_library/read_string_as_command.wdl +17 -0
  190. toil/test/wdl/standard_library/read_tsv.json +3 -0
  191. toil/test/wdl/standard_library/read_tsv_as_output.wdl +31 -0
  192. toil/test/wdl/standard_library/round.json +3 -0
  193. toil/test/wdl/standard_library/round_as_command.wdl +16 -0
  194. toil/test/wdl/standard_library/round_as_input.wdl +16 -0
  195. toil/test/wdl/standard_library/size.json +3 -0
  196. toil/test/wdl/standard_library/size_as_command.wdl +17 -0
  197. toil/test/wdl/standard_library/size_as_output.wdl +36 -0
  198. toil/test/wdl/standard_library/stderr.json +3 -0
  199. toil/test/wdl/standard_library/stderr_as_output.wdl +30 -0
  200. toil/test/wdl/standard_library/stdout.json +3 -0
  201. toil/test/wdl/standard_library/stdout_as_output.wdl +30 -0
  202. toil/test/wdl/standard_library/sub.json +3 -0
  203. toil/test/wdl/standard_library/sub_as_input.wdl +17 -0
  204. toil/test/wdl/standard_library/sub_as_input_with_file.wdl +17 -0
  205. toil/test/wdl/standard_library/transpose.json +6 -0
  206. toil/test/wdl/standard_library/transpose_as_input.wdl +18 -0
  207. toil/test/wdl/standard_library/write_json.json +6 -0
  208. toil/test/wdl/standard_library/write_json_as_command.wdl +17 -0
  209. toil/test/wdl/standard_library/write_lines.json +7 -0
  210. toil/test/wdl/standard_library/write_lines_as_command.wdl +17 -0
  211. toil/test/wdl/standard_library/write_map.json +6 -0
  212. toil/test/wdl/standard_library/write_map_as_command.wdl +17 -0
  213. toil/test/wdl/standard_library/write_tsv.json +6 -0
  214. toil/test/wdl/standard_library/write_tsv_as_command.wdl +17 -0
  215. toil/test/wdl/standard_library/zip.json +12 -0
  216. toil/test/wdl/standard_library/zip_as_input.wdl +19 -0
  217. toil/test/wdl/test.csv +3 -0
  218. toil/test/wdl/test.tsv +3 -0
  219. toil/test/wdl/testfiles/croo.wdl +38 -0
  220. toil/test/wdl/testfiles/drop_files.wdl +62 -0
  221. toil/test/wdl/testfiles/drop_files_subworkflow.wdl +13 -0
  222. toil/test/wdl/testfiles/empty.txt +0 -0
  223. toil/test/wdl/testfiles/not_enough_outputs.wdl +33 -0
  224. toil/test/wdl/testfiles/random.wdl +66 -0
  225. toil/test/wdl/testfiles/string_file_coercion.json +1 -0
  226. toil/test/wdl/testfiles/string_file_coercion.wdl +35 -0
  227. toil/test/wdl/testfiles/test.json +4 -0
  228. toil/test/wdl/testfiles/test_boolean.txt +1 -0
  229. toil/test/wdl/testfiles/test_float.txt +1 -0
  230. toil/test/wdl/testfiles/test_int.txt +1 -0
  231. toil/test/wdl/testfiles/test_lines.txt +5 -0
  232. toil/test/wdl/testfiles/test_map.txt +2 -0
  233. toil/test/wdl/testfiles/test_string.txt +1 -0
  234. toil/test/wdl/testfiles/url_to_file.wdl +13 -0
  235. toil/test/wdl/testfiles/url_to_optional_file.wdl +13 -0
  236. toil/test/wdl/testfiles/vocab.json +1 -0
  237. toil/test/wdl/testfiles/vocab.wdl +66 -0
  238. toil/test/wdl/testfiles/wait.wdl +34 -0
  239. toil/test/wdl/wdl_specification/type_pair.json +23 -0
  240. toil/test/wdl/wdl_specification/type_pair_basic.wdl +36 -0
  241. toil/test/wdl/wdl_specification/type_pair_with_files.wdl +36 -0
  242. toil/test/wdl/wdl_specification/v1_spec.json +1 -0
  243. toil/test/wdl/wdl_specification/v1_spec_declaration.wdl +39 -0
  244. toil/test/wdl/wdltoil_test.py +680 -407
  245. toil/test/wdl/wdltoil_test_kubernetes.py +2 -2
  246. toil/version.py +9 -9
  247. toil/wdl/wdltoil.py +336 -123
  248. {toil-8.1.0b1.dist-info → toil-8.2.0.dist-info}/METADATA +5 -4
  249. toil-8.2.0.dist-info/RECORD +439 -0
  250. {toil-8.1.0b1.dist-info → toil-8.2.0.dist-info}/WHEEL +1 -1
  251. toil-8.1.0b1.dist-info/RECORD +0 -259
  252. {toil-8.1.0b1.dist-info → toil-8.2.0.dist-info}/entry_points.txt +0 -0
  253. {toil-8.1.0b1.dist-info → toil-8.2.0.dist-info/licenses}/LICENSE +0 -0
  254. {toil-8.1.0b1.dist-info → toil-8.2.0.dist-info}/top_level.txt +0 -0
toil-8.1.0b1.dist-info/RECORD DELETED
@@ -1,259 +0,0 @@
1
- toil/__init__.py,sha256=lOuyAgzwG9OmmOOqvxMOQCUfDU50sudUjUlHvp3aHns,19330
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- toil/bus.py,sha256=Hi2TTCVGX4WTw67BOKo7l9yZw9Ln_zcobJzQxrfge4M,29938
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- toil/common.py,sha256=MR-AUVmQhNHmN1IqlXTHMNzAbMA8JvwDfXzcgxJCjJ8,81333
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- toil/deferred.py,sha256=2ShsuPqDwu0jhBQ6ocMwe4lfNegBm2lj7dOG9E7X3Zc,14152
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- toil/exceptions.py,sha256=oL2d9uutwtcPkMcEUGrixKUd4y1JLSA0-N7hNJqCLSk,1883
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- toil/job.py,sha256=w31q56P7pq6yvJpoH6mTQU3l0GBsm_O0jnDi5zpGQqI,173735
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- toil/leader.py,sha256=ubIdkEUb3hmGAc7oCWnKuvxOAlyyvOgVyDCN4i6DJAw,85101
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- toil/realtimeLogger.py,sha256=2O4AUaKtvItzzCAQKORIEHZ2cDoLf_6njoKWv_uzdFc,9878
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- toil/resource.py,sha256=PlI6R28aYqfYLDsztjlAYpkVGfSr2O0DhrgDXpXJxa0,25650
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- toil/serviceManager.py,sha256=GE5IUjQmNrekYv9tclim0RlCFf4ueOQ2H4qHjMBrOcg,19978
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- toil/statsAndLogging.py,sha256=JXir7TCV8OdDaAdt3VsDR2rbdNWk4ILyOwlKHVdoXT0,18696
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- toil/toilState.py,sha256=DD52XQv8wRCYzF7-F6Olqa_k6u-_py-JWyjqJHRh6Z0,17989
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- toil/version.py,sha256=_Xxx7pjBP8pHk7CZP_gx3EuetyVeDsi9SWhpZw7Ux3s,494
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- toil/worker.py,sha256=ywdN4v8qz5CuNQgMJcOlOsVj7BcdqdWuoTp6mFCnE0Y,38967
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- toil/batchSystems/__init__.py,sha256=T8psI5GmvE71_XmajKsfeQ3YUs6XM7rX1Fy9VNUX_-Q,1036
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- toil/batchSystems/abstractBatchSystem.py,sha256=h8mbA_k_7EZqOrbcdQmKHDcAy6D2ZB77XXS3Wu4-E90,33542
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- toil/batchSystems/abstractGridEngineBatchSystem.py,sha256=yR3nlCvJRcxYEDRyA3qYuNjvgmVDfzvW4bx9RY14TLg,24336
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- toil/batchSystems/awsBatch.py,sha256=vpV6CxUBi0sj5b91cWKi7Gonk276Nfz0_-QLZVoahNQ,27298
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- toil/batchSystems/cleanup_support.py,sha256=mpExAW-Tw2ZnGMgJEt06zZGjNLhXHPLVuDEraM9N8r4,4054
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- toil/batchSystems/contained_executor.py,sha256=2wP3sDyOanB2YrXxhdJ1PI3VohKK37ifgRya2F0rcMY,5111
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- toil/batchSystems/gridengine.py,sha256=OL1SOQXV5vz7UwNSSZ2lKTRArkeaVRND5FyqQ8K8V20,8114
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- toil/batchSystems/htcondor.py,sha256=nCylLUvRyX2k79LYriJgwhmowJBRekBWYUSpJgtawsY,18613
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- toil/batchSystems/kubernetes.py,sha256=5bC_ipdfgIzl2_I1SxqrcRHPjbcicBNznNK2c3u0gnY,86959
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- toil/batchSystems/local_support.py,sha256=R-DT_G5jcQXjZyDQ9OdFj0KUeULMSmcLBen3p-tSGdw,3893
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- toil/batchSystems/lsf.py,sha256=rQJe6dpnqs-LAZ0qaAo94VtxvhADwv8XzRTrQulp-mQ,18089
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- toil/batchSystems/lsfHelper.py,sha256=IE5y-x-Mofau7jksWjBdTLt5dVvyj-w8dd3gqwZ-r8o,7227
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- toil/batchSystems/options.py,sha256=HZ4nI2paKxulcWOd81R3p_j7BE4j2U9ZjWehDKaoyaA,8155
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- toil/batchSystems/registry.py,sha256=eizqlhn4AdBzykdOFu_S5ZcU4eYpMB_vDTb8ml6W3Kw,6701
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