LICENSE
MANIFEST.in
README.rst
requirements-aws.txt
requirements-cwl.txt
requirements-dev.txt
requirements-encryption.txt
requirements-google.txt
requirements-htcondor.txt
requirements-kubernetes.txt
requirements-mesos.txt
requirements-server.txt
requirements-wdl.txt
requirements.txt
setup.cfg
setup.py
src/toil/__init__.py
src/toil/bus.py
src/toil/common.py
src/toil/deferred.py
src/toil/exceptions.py
src/toil/job.py
src/toil/leader.py
src/toil/realtimeLogger.py
src/toil/resource.py
src/toil/serviceManager.py
src/toil/statsAndLogging.py
src/toil/toilState.py
src/toil/version.py
src/toil/worker.py
src/toil.egg-info/PKG-INFO
src/toil.egg-info/SOURCES.txt
src/toil.egg-info/dependency_links.txt
src/toil.egg-info/entry_points.txt
src/toil.egg-info/requires.txt
src/toil.egg-info/top_level.txt
src/toil/batchSystems/__init__.py
src/toil/batchSystems/abstractBatchSystem.py
src/toil/batchSystems/abstractGridEngineBatchSystem.py
src/toil/batchSystems/awsBatch.py
src/toil/batchSystems/cleanup_support.py
src/toil/batchSystems/contained_executor.py
src/toil/batchSystems/gridengine.py
src/toil/batchSystems/htcondor.py
src/toil/batchSystems/kubernetes.py
src/toil/batchSystems/local_support.py
src/toil/batchSystems/lsf.py
src/toil/batchSystems/lsfHelper.py
src/toil/batchSystems/options.py
src/toil/batchSystems/registry.py
src/toil/batchSystems/singleMachine.py
src/toil/batchSystems/slurm.py
src/toil/batchSystems/torque.py
src/toil/batchSystems/mesos/__init__.py
src/toil/batchSystems/mesos/batchSystem.py
src/toil/batchSystems/mesos/conftest.py
src/toil/batchSystems/mesos/executor.py
src/toil/batchSystems/mesos/test/__init__.py
src/toil/cwl/__init__.py
src/toil/cwl/conftest.py
src/toil/cwl/cwltoil.py
src/toil/cwl/utils.py
src/toil/fileStores/__init__.py
src/toil/fileStores/abstractFileStore.py
src/toil/fileStores/cachingFileStore.py
src/toil/fileStores/nonCachingFileStore.py
src/toil/jobStores/__init__.py
src/toil/jobStores/abstractJobStore.py
src/toil/jobStores/conftest.py
src/toil/jobStores/fileJobStore.py
src/toil/jobStores/googleJobStore.py
src/toil/jobStores/utils.py
src/toil/jobStores/aws/__init__.py
src/toil/jobStores/aws/jobStore.py
src/toil/jobStores/aws/utils.py
src/toil/lib/__init__.py
src/toil/lib/accelerators.py
src/toil/lib/bioio.py
src/toil/lib/compatibility.py
src/toil/lib/conversions.py
src/toil/lib/docker.py
src/toil/lib/ec2.py
src/toil/lib/ec2nodes.py
src/toil/lib/exceptions.py
src/toil/lib/expando.py
src/toil/lib/generatedEC2Lists.py
src/toil/lib/humanize.py
src/toil/lib/io.py
src/toil/lib/iterables.py
src/toil/lib/memoize.py
src/toil/lib/misc.py
src/toil/lib/objects.py
src/toil/lib/resources.py
src/toil/lib/retry.py
src/toil/lib/threading.py
src/toil/lib/throttle.py
src/toil/lib/aws/__init__.py
src/toil/lib/aws/ami.py
src/toil/lib/aws/iam.py
src/toil/lib/aws/session.py
src/toil/lib/aws/utils.py
src/toil/lib/encryption/__init__.py
src/toil/lib/encryption/_dummy.py
src/toil/lib/encryption/_nacl.py
src/toil/lib/encryption/conftest.py
src/toil/options/__init__.py
src/toil/options/common.py
src/toil/options/cwl.py
src/toil/options/wdl.py
src/toil/provisioners/__init__.py
src/toil/provisioners/abstractProvisioner.py
src/toil/provisioners/clusterScaler.py
src/toil/provisioners/gceProvisioner.py
src/toil/provisioners/node.py
src/toil/provisioners/aws/__init__.py
src/toil/provisioners/aws/awsProvisioner.py
src/toil/server/__init__.py
src/toil/server/app.py
src/toil/server/celery_app.py
src/toil/server/utils.py
src/toil/server/wsgi_app.py
src/toil/server/api_spec/__init__.py
src/toil/server/api_spec/workflow_execution_service.swagger.yaml
src/toil/server/cli/__init__.py
src/toil/server/cli/wes_cwl_runner.py
src/toil/server/wes/__init__.py
src/toil/server/wes/abstract_backend.py
src/toil/server/wes/amazon_wes_utils.py
src/toil/server/wes/tasks.py
src/toil/server/wes/toil_backend.py
src/toil/test/__init__.py
src/toil/test/batchSystems/__init__.py
src/toil/test/batchSystems/batchSystemTest.py
src/toil/test/batchSystems/test_lsf_helper.py
src/toil/test/batchSystems/test_slurm.py
src/toil/test/cactus/__init__.py
src/toil/test/cactus/test_cactus_integration.py
src/toil/test/cwl/__init__.py
src/toil/test/cwl/alwaysfails.cwl
src/toil/test/cwl/colon_test_output.cwl
src/toil/test/cwl/colon_test_output_job.yaml
src/toil/test/cwl/conditional_wf.cwl
src/toil/test/cwl/conditional_wf.yaml
src/toil/test/cwl/conftest.py
src/toil/test/cwl/cwlTest.py
src/toil/test/cwl/directory_from_directory.cwl
src/toil/test/cwl/download.cwl
src/toil/test/cwl/download_directory.cwl
src/toil/test/cwl/download_subdirectory.cwl
src/toil/test/cwl/echo-stderr.cwl
src/toil/test/cwl/echo-stdout-log-dir.cwl
src/toil/test/cwl/echo.cwl
src/toil/test/cwl/echo_string.cwl
src/toil/test/cwl/echo_string_scatter_capture_stdout.cwl
src/toil/test/cwl/file_from_directory.cwl
src/toil/test/cwl/glob_dir.cwl
src/toil/test/cwl/load_contents.cwl
src/toil/test/cwl/mpi_simple.cwl
src/toil/test/cwl/nvidia_smi.cwl
src/toil/test/cwl/preemptible.cwl
src/toil/test/cwl/preemptible_expression.cwl
src/toil/test/cwl/revsort.cwl
src/toil/test/cwl/revsort2.cwl
src/toil/test/cwl/revtool.cwl
src/toil/test/cwl/revtool2.cwl
src/toil/test/cwl/s3_secondary_file.cwl
src/toil/test/cwl/seqtk_seq.cwl
src/toil/test/cwl/sorttool.cwl
src/toil/test/cwl/stream.cwl
src/toil/test/cwl/test_filename_conflict_detection.cwl
src/toil/test/cwl/test_filename_conflict_detection_at_root.cwl
src/toil/test/cwl/test_filename_conflict_resolution.cwl
src/toil/test/docs/__init__.py
src/toil/test/docs/scriptsTest.py
src/toil/test/jobStores/__init__.py
src/toil/test/jobStores/jobStoreTest.py
src/toil/test/lib/__init__.py
src/toil/test/lib/dockerTest.py
src/toil/test/lib/test_conversions.py
src/toil/test/lib/test_ec2.py
src/toil/test/lib/test_misc.py
src/toil/test/lib/aws/__init__.py
src/toil/test/lib/aws/test_iam.py
src/toil/test/lib/aws/test_s3.py
src/toil/test/lib/aws/test_utils.py
src/toil/test/mesos/MesosDataStructuresTest.py
src/toil/test/mesos/__init__.py
src/toil/test/mesos/helloWorld.py
src/toil/test/mesos/stress.py
src/toil/test/options/__init__.py
src/toil/test/options/options.py
src/toil/test/provisioners/__init__.py
src/toil/test/provisioners/clusterScalerTest.py
src/toil/test/provisioners/clusterTest.py
src/toil/test/provisioners/gceProvisionerTest.py
src/toil/test/provisioners/provisionerTest.py
src/toil/test/provisioners/restartScript.py
src/toil/test/provisioners/aws/__init__.py
src/toil/test/provisioners/aws/awsProvisionerTest.py
src/toil/test/server/__init__.py
src/toil/test/server/serverTest.py
src/toil/test/sort/__init__.py
src/toil/test/sort/restart_sort.py
src/toil/test/sort/sort.py
src/toil/test/sort/sortTest.py
src/toil/test/src/__init__.py
src/toil/test/src/autoDeploymentTest.py
src/toil/test/src/busTest.py
src/toil/test/src/checkpointTest.py
src/toil/test/src/deferredFunctionTest.py
src/toil/test/src/dockerCheckTest.py
src/toil/test/src/fileStoreTest.py
src/toil/test/src/helloWorldTest.py
src/toil/test/src/importExportFileTest.py
src/toil/test/src/jobDescriptionTest.py
src/toil/test/src/jobEncapsulationTest.py
src/toil/test/src/jobFileStoreTest.py
src/toil/test/src/jobServiceTest.py
src/toil/test/src/jobTest.py
src/toil/test/src/miscTests.py
src/toil/test/src/promisedRequirementTest.py
src/toil/test/src/promisesTest.py
src/toil/test/src/realtimeLoggerTest.py
src/toil/test/src/regularLogTest.py
src/toil/test/src/resourceTest.py
src/toil/test/src/restartDAGTest.py
src/toil/test/src/resumabilityTest.py
src/toil/test/src/retainTempDirTest.py
src/toil/test/src/systemTest.py
src/toil/test/src/threadingTest.py
src/toil/test/src/toilContextManagerTest.py
src/toil/test/src/userDefinedJobArgTypeTest.py
src/toil/test/src/workerTest.py
src/toil/test/utils/__init__.py
src/toil/test/utils/toilDebugTest.py
src/toil/test/utils/toilKillTest.py
src/toil/test/utils/utilsTest.py
src/toil/test/wdl/__init__.py
src/toil/test/wdl/wdltoil_test.py
src/toil/utils/__init__.py
src/toil/utils/toilClean.py
src/toil/utils/toilConfig.py
src/toil/utils/toilDebugFile.py
src/toil/utils/toilDebugJob.py
src/toil/utils/toilDestroyCluster.py
src/toil/utils/toilKill.py
src/toil/utils/toilLaunchCluster.py
src/toil/utils/toilMain.py
src/toil/utils/toilRsyncCluster.py
src/toil/utils/toilServer.py
src/toil/utils/toilSshCluster.py
src/toil/utils/toilStats.py
src/toil/utils/toilStatus.py
src/toil/utils/toilUpdateEC2Instances.py
src/toil/wdl/__init__.py
src/toil/wdl/utils.py
src/toil/wdl/wdltoil.py