├── .appveyor.yml ├── .gitattributes ├── .gitignore ├── .travis.yml ├── README.md ├── pyflow ├── COPYRIGHT.txt ├── README.md ├── demo │ ├── README.txt │ ├── bclToBwaBam │ │ ├── README.txt │ │ ├── bwaworkflow.py │ │ ├── configBclToBwaBam.py │ │ ├── configBclToBwaBam.py.ini │ │ └── example_configuration.bash │ ├── cwdDemo │ │ └── cwdDemo.py │ ├── envDemo │ │ └── envDemo.py │ ├── helloWorld │ │ ├── README.txt │ │ └── helloWorld.py │ ├── launchTasksUntil │ │ ├── README.md │ │ ├── launchTasksUntil.py │ │ └── testWorker.py │ ├── makeDemo │ │ ├── .hidden │ │ └── makeDemo.py │ ├── memoryDemo │ │ └── memoryDemo.py │ ├── mutexDemo │ │ ├── mutexDemo.py │ │ └── testtasks │ │ │ └── sleeper.bash │ ├── retryDemo │ │ └── retryDemo.py │ ├── runOptionsDemo │ │ ├── getDemoRunOptions.py │ │ ├── runOptionsDemo.py │ │ └── testtasks │ │ │ ├── sleeper.bash │ │ │ └── yeller.bash │ ├── simpleDemo │ │ ├── simpleDemo.py │ │ └── testtasks │ │ │ ├── runner.bash │ │ │ ├── runner.c │ │ │ ├── sleeper.bash │ │ │ └── yeller.bash │ ├── subWorkflow │ │ ├── subWorkflow.py │ │ └── testtasks │ │ │ ├── runner.bash │ │ │ ├── runner.c │ │ │ ├── sleeper.bash │ │ │ └── yeller.bash │ └── successMsgDemo │ │ └── successMsgDemo.py ├── doc │ ├── ChangeLog.txt │ ├── README.txt │ ├── client_api │ │ ├── README │ │ ├── make_WorkflowRunner_API_html_doc.bash │ │ └── make_WorkflowRunner_API_simple_doc.py │ └── developer │ │ ├── README │ │ └── make_pyflow_developer_html_doc.bash ├── setup.py └── src │ ├── __init__.py │ ├── pyflow.py │ ├── pyflowConfig.py │ └── pyflowTaskWrapper.py └── scratch ├── README.txt ├── bench ├── README.md └── manyThreads.py ├── make_release_tarball.bash ├── notes ├── design.notes └── todo ├── pybox ├── email_test.py ├── hijack.py ├── inspect.py └── memTest.py ├── run_source_check_and_format.bash ├── source_check_and_format ├── delete_trailing_wspace.bash ├── ensureFileEndsInNewline.py └── source_header_scripts │ ├── new_header │ ├── reheader_all_source.bash │ └── reheader_script_file.py └── test ├── README.md ├── pyflow_basic_feature_runner.py ├── pyflow_unit_tests.py ├── test_pyflow.py ├── test_release_tarball.bash └── testtasks ├── runner.bash ├── runner.c ├── sleeper.bash ├── slow_yeller.py └── yeller.bash /.appveyor.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Illumina/pyflow/HEAD/.appveyor.yml -------------------------------------------------------------------------------- /.gitattributes: -------------------------------------------------------------------------------- 1 | pyflow/README.txt export-subst 2 | -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- 1 | *.pyc 2 | *~ 3 | pyflow.data 4 | -------------------------------------------------------------------------------- /.travis.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Illumina/pyflow/HEAD/.travis.yml -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Illumina/pyflow/HEAD/README.md -------------------------------------------------------------------------------- /pyflow/COPYRIGHT.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Illumina/pyflow/HEAD/pyflow/COPYRIGHT.txt -------------------------------------------------------------------------------- /pyflow/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Illumina/pyflow/HEAD/pyflow/README.md -------------------------------------------------------------------------------- /pyflow/demo/README.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Illumina/pyflow/HEAD/pyflow/demo/README.txt -------------------------------------------------------------------------------- /pyflow/demo/bclToBwaBam/README.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Illumina/pyflow/HEAD/pyflow/demo/bclToBwaBam/README.txt -------------------------------------------------------------------------------- /pyflow/demo/bclToBwaBam/bwaworkflow.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Illumina/pyflow/HEAD/pyflow/demo/bclToBwaBam/bwaworkflow.py -------------------------------------------------------------------------------- /pyflow/demo/bclToBwaBam/configBclToBwaBam.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Illumina/pyflow/HEAD/pyflow/demo/bclToBwaBam/configBclToBwaBam.py -------------------------------------------------------------------------------- /pyflow/demo/bclToBwaBam/configBclToBwaBam.py.ini: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Illumina/pyflow/HEAD/pyflow/demo/bclToBwaBam/configBclToBwaBam.py.ini -------------------------------------------------------------------------------- /pyflow/demo/bclToBwaBam/example_configuration.bash: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Illumina/pyflow/HEAD/pyflow/demo/bclToBwaBam/example_configuration.bash -------------------------------------------------------------------------------- /pyflow/demo/cwdDemo/cwdDemo.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Illumina/pyflow/HEAD/pyflow/demo/cwdDemo/cwdDemo.py -------------------------------------------------------------------------------- /pyflow/demo/envDemo/envDemo.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Illumina/pyflow/HEAD/pyflow/demo/envDemo/envDemo.py -------------------------------------------------------------------------------- /pyflow/demo/helloWorld/README.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Illumina/pyflow/HEAD/pyflow/demo/helloWorld/README.txt -------------------------------------------------------------------------------- /pyflow/demo/helloWorld/helloWorld.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Illumina/pyflow/HEAD/pyflow/demo/helloWorld/helloWorld.py -------------------------------------------------------------------------------- /pyflow/demo/launchTasksUntil/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Illumina/pyflow/HEAD/pyflow/demo/launchTasksUntil/README.md -------------------------------------------------------------------------------- /pyflow/demo/launchTasksUntil/launchTasksUntil.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Illumina/pyflow/HEAD/pyflow/demo/launchTasksUntil/launchTasksUntil.py -------------------------------------------------------------------------------- /pyflow/demo/launchTasksUntil/testWorker.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Illumina/pyflow/HEAD/pyflow/demo/launchTasksUntil/testWorker.py -------------------------------------------------------------------------------- /pyflow/demo/makeDemo/.hidden: -------------------------------------------------------------------------------- 1 | 2 | .PHONY: A B 3 | A: B 4 | @echo "Made it!" 5 | 6 | B: 7 | sleep 5 8 | -------------------------------------------------------------------------------- /pyflow/demo/makeDemo/makeDemo.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Illumina/pyflow/HEAD/pyflow/demo/makeDemo/makeDemo.py -------------------------------------------------------------------------------- /pyflow/demo/memoryDemo/memoryDemo.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Illumina/pyflow/HEAD/pyflow/demo/memoryDemo/memoryDemo.py -------------------------------------------------------------------------------- /pyflow/demo/mutexDemo/mutexDemo.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Illumina/pyflow/HEAD/pyflow/demo/mutexDemo/mutexDemo.py -------------------------------------------------------------------------------- /pyflow/demo/mutexDemo/testtasks/sleeper.bash: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Illumina/pyflow/HEAD/pyflow/demo/mutexDemo/testtasks/sleeper.bash -------------------------------------------------------------------------------- /pyflow/demo/retryDemo/retryDemo.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Illumina/pyflow/HEAD/pyflow/demo/retryDemo/retryDemo.py -------------------------------------------------------------------------------- /pyflow/demo/runOptionsDemo/getDemoRunOptions.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Illumina/pyflow/HEAD/pyflow/demo/runOptionsDemo/getDemoRunOptions.py -------------------------------------------------------------------------------- /pyflow/demo/runOptionsDemo/runOptionsDemo.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Illumina/pyflow/HEAD/pyflow/demo/runOptionsDemo/runOptionsDemo.py -------------------------------------------------------------------------------- /pyflow/demo/runOptionsDemo/testtasks/sleeper.bash: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Illumina/pyflow/HEAD/pyflow/demo/runOptionsDemo/testtasks/sleeper.bash -------------------------------------------------------------------------------- /pyflow/demo/runOptionsDemo/testtasks/yeller.bash: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Illumina/pyflow/HEAD/pyflow/demo/runOptionsDemo/testtasks/yeller.bash -------------------------------------------------------------------------------- /pyflow/demo/simpleDemo/simpleDemo.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Illumina/pyflow/HEAD/pyflow/demo/simpleDemo/simpleDemo.py -------------------------------------------------------------------------------- /pyflow/demo/simpleDemo/testtasks/runner.bash: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Illumina/pyflow/HEAD/pyflow/demo/simpleDemo/testtasks/runner.bash -------------------------------------------------------------------------------- /pyflow/demo/simpleDemo/testtasks/runner.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Illumina/pyflow/HEAD/pyflow/demo/simpleDemo/testtasks/runner.c -------------------------------------------------------------------------------- /pyflow/demo/simpleDemo/testtasks/sleeper.bash: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Illumina/pyflow/HEAD/pyflow/demo/simpleDemo/testtasks/sleeper.bash -------------------------------------------------------------------------------- /pyflow/demo/simpleDemo/testtasks/yeller.bash: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Illumina/pyflow/HEAD/pyflow/demo/simpleDemo/testtasks/yeller.bash -------------------------------------------------------------------------------- /pyflow/demo/subWorkflow/subWorkflow.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Illumina/pyflow/HEAD/pyflow/demo/subWorkflow/subWorkflow.py -------------------------------------------------------------------------------- /pyflow/demo/subWorkflow/testtasks/runner.bash: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Illumina/pyflow/HEAD/pyflow/demo/subWorkflow/testtasks/runner.bash -------------------------------------------------------------------------------- /pyflow/demo/subWorkflow/testtasks/runner.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Illumina/pyflow/HEAD/pyflow/demo/subWorkflow/testtasks/runner.c -------------------------------------------------------------------------------- /pyflow/demo/subWorkflow/testtasks/sleeper.bash: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Illumina/pyflow/HEAD/pyflow/demo/subWorkflow/testtasks/sleeper.bash -------------------------------------------------------------------------------- /pyflow/demo/subWorkflow/testtasks/yeller.bash: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Illumina/pyflow/HEAD/pyflow/demo/subWorkflow/testtasks/yeller.bash -------------------------------------------------------------------------------- /pyflow/demo/successMsgDemo/successMsgDemo.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Illumina/pyflow/HEAD/pyflow/demo/successMsgDemo/successMsgDemo.py -------------------------------------------------------------------------------- /pyflow/doc/ChangeLog.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Illumina/pyflow/HEAD/pyflow/doc/ChangeLog.txt -------------------------------------------------------------------------------- /pyflow/doc/README.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Illumina/pyflow/HEAD/pyflow/doc/README.txt -------------------------------------------------------------------------------- /pyflow/doc/client_api/README: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Illumina/pyflow/HEAD/pyflow/doc/client_api/README -------------------------------------------------------------------------------- /pyflow/doc/client_api/make_WorkflowRunner_API_html_doc.bash: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Illumina/pyflow/HEAD/pyflow/doc/client_api/make_WorkflowRunner_API_html_doc.bash -------------------------------------------------------------------------------- /pyflow/doc/client_api/make_WorkflowRunner_API_simple_doc.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Illumina/pyflow/HEAD/pyflow/doc/client_api/make_WorkflowRunner_API_simple_doc.py -------------------------------------------------------------------------------- /pyflow/doc/developer/README: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Illumina/pyflow/HEAD/pyflow/doc/developer/README -------------------------------------------------------------------------------- /pyflow/doc/developer/make_pyflow_developer_html_doc.bash: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Illumina/pyflow/HEAD/pyflow/doc/developer/make_pyflow_developer_html_doc.bash -------------------------------------------------------------------------------- /pyflow/setup.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Illumina/pyflow/HEAD/pyflow/setup.py -------------------------------------------------------------------------------- /pyflow/src/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Illumina/pyflow/HEAD/pyflow/src/__init__.py -------------------------------------------------------------------------------- /pyflow/src/pyflow.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Illumina/pyflow/HEAD/pyflow/src/pyflow.py -------------------------------------------------------------------------------- /pyflow/src/pyflowConfig.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Illumina/pyflow/HEAD/pyflow/src/pyflowConfig.py -------------------------------------------------------------------------------- /pyflow/src/pyflowTaskWrapper.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Illumina/pyflow/HEAD/pyflow/src/pyflowTaskWrapper.py -------------------------------------------------------------------------------- /scratch/README.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Illumina/pyflow/HEAD/scratch/README.txt -------------------------------------------------------------------------------- /scratch/bench/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Illumina/pyflow/HEAD/scratch/bench/README.md -------------------------------------------------------------------------------- /scratch/bench/manyThreads.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Illumina/pyflow/HEAD/scratch/bench/manyThreads.py -------------------------------------------------------------------------------- /scratch/make_release_tarball.bash: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Illumina/pyflow/HEAD/scratch/make_release_tarball.bash -------------------------------------------------------------------------------- /scratch/notes/design.notes: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Illumina/pyflow/HEAD/scratch/notes/design.notes -------------------------------------------------------------------------------- /scratch/notes/todo: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Illumina/pyflow/HEAD/scratch/notes/todo -------------------------------------------------------------------------------- /scratch/pybox/email_test.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Illumina/pyflow/HEAD/scratch/pybox/email_test.py -------------------------------------------------------------------------------- /scratch/pybox/hijack.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Illumina/pyflow/HEAD/scratch/pybox/hijack.py -------------------------------------------------------------------------------- /scratch/pybox/inspect.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Illumina/pyflow/HEAD/scratch/pybox/inspect.py -------------------------------------------------------------------------------- /scratch/pybox/memTest.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Illumina/pyflow/HEAD/scratch/pybox/memTest.py -------------------------------------------------------------------------------- /scratch/run_source_check_and_format.bash: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Illumina/pyflow/HEAD/scratch/run_source_check_and_format.bash -------------------------------------------------------------------------------- /scratch/source_check_and_format/delete_trailing_wspace.bash: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Illumina/pyflow/HEAD/scratch/source_check_and_format/delete_trailing_wspace.bash -------------------------------------------------------------------------------- /scratch/source_check_and_format/ensureFileEndsInNewline.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Illumina/pyflow/HEAD/scratch/source_check_and_format/ensureFileEndsInNewline.py -------------------------------------------------------------------------------- /scratch/source_check_and_format/source_header_scripts/new_header: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Illumina/pyflow/HEAD/scratch/source_check_and_format/source_header_scripts/new_header -------------------------------------------------------------------------------- /scratch/source_check_and_format/source_header_scripts/reheader_all_source.bash: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Illumina/pyflow/HEAD/scratch/source_check_and_format/source_header_scripts/reheader_all_source.bash -------------------------------------------------------------------------------- /scratch/source_check_and_format/source_header_scripts/reheader_script_file.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Illumina/pyflow/HEAD/scratch/source_check_and_format/source_header_scripts/reheader_script_file.py -------------------------------------------------------------------------------- /scratch/test/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Illumina/pyflow/HEAD/scratch/test/README.md -------------------------------------------------------------------------------- /scratch/test/pyflow_basic_feature_runner.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Illumina/pyflow/HEAD/scratch/test/pyflow_basic_feature_runner.py -------------------------------------------------------------------------------- /scratch/test/pyflow_unit_tests.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Illumina/pyflow/HEAD/scratch/test/pyflow_unit_tests.py -------------------------------------------------------------------------------- /scratch/test/test_pyflow.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Illumina/pyflow/HEAD/scratch/test/test_pyflow.py -------------------------------------------------------------------------------- /scratch/test/test_release_tarball.bash: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Illumina/pyflow/HEAD/scratch/test/test_release_tarball.bash -------------------------------------------------------------------------------- /scratch/test/testtasks/runner.bash: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Illumina/pyflow/HEAD/scratch/test/testtasks/runner.bash -------------------------------------------------------------------------------- /scratch/test/testtasks/runner.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Illumina/pyflow/HEAD/scratch/test/testtasks/runner.c -------------------------------------------------------------------------------- /scratch/test/testtasks/sleeper.bash: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Illumina/pyflow/HEAD/scratch/test/testtasks/sleeper.bash -------------------------------------------------------------------------------- /scratch/test/testtasks/slow_yeller.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Illumina/pyflow/HEAD/scratch/test/testtasks/slow_yeller.py -------------------------------------------------------------------------------- /scratch/test/testtasks/yeller.bash: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Illumina/pyflow/HEAD/scratch/test/testtasks/yeller.bash --------------------------------------------------------------------------------