CHANGES.TXT
LICENSE.TXT
MANIFEST.in
README.rst
USAGE.TXT
setup.py
doc/Makefile
doc/cheatsheet.rst
doc/conf.py
doc/contents.rst
doc/contributing.rst
doc/design.rst
doc/faq.rst
doc/gallery.rst
doc/global.inc
doc/glossary.rst
doc/history.rst
doc/implementation_notes.rst
doc/installation.rst
doc/make.bat
doc/manual_follows1.png
doc/pipeline_functions.rst
doc/propset
doc/proxy_logger.rst
doc/regenerate_figures
doc/release.rst
doc/task.rst
doc/todo.rst
doc/why_ruffus.rst
doc/_templates/index.html
doc/_templates/layout.html
doc/complex_dags/dot/all.dot
doc/complex_dags/dot/non_dag.dot
doc/complex_dags/dot/task17.dot
doc/complex_dags/dot/task17_from_task9.dot
doc/complex_dags/dot/task25_from_task9.dot
doc/complex_dags/jpg/all.jpg
doc/complex_dags/jpg/all_sm.jpg
doc/complex_dags/jpg/non_dag.jpg
doc/complex_dags/jpg/non_dag_sm.jpg
doc/complex_dags/jpg/task17.jpg
doc/complex_dags/jpg/task17_from_task9.jpg
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doc/complex_dags/jpg/task17_sm.jpg
doc/complex_dags/jpg/task25_from_task9.jpg
doc/complex_dags/jpg/task25_from_task9_sm.jpg
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doc/decorators/active_if.rst
doc/decorators/check_if_uptodate.rst
doc/decorators/collate.rst
doc/decorators/combinations.rst
doc/decorators/combinations_with_replacement.rst
doc/decorators/decorators.rst
doc/decorators/files.rst
doc/decorators/files_ex.rst
doc/decorators/files_re.rst
doc/decorators/follows.rst
doc/decorators/graphviz.rst
doc/decorators/indicator_objects.rst
doc/decorators/jobs_limit.rst
doc/decorators/merge.rst
doc/decorators/mkdir.rst
doc/decorators/originate.rst
doc/decorators/parallel.rst
doc/decorators/permutations.rst
doc/decorators/posttask.rst
doc/decorators/product.rst
doc/decorators/split.rst
doc/decorators/subdivide.rst
doc/decorators/todo.sphinx
doc/decorators/transform.rst
doc/decorators/transform_ex.rst
doc/examples/paired_end_data.py.rst
doc/examples/bioinformatics/index.rst
doc/examples/bioinformatics/part1_code.rst
doc/examples/bioinformatics/part2.rst
doc/examples/bioinformatics/part2_code.rst
doc/images/bestiary_combinatorics.png
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doc/images/bestiary_transform.png
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doc/images/design.task_based_workflow.dot
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doc/images/examples_bioinformatics_complete.jpg
doc/images/examples_bioinformatics_error.png
doc/images/examples_bioinformatics_merge.jpg
doc/images/examples_bioinformatics_pipeline.jpg
doc/images/examples_bioinformatics_split.jpg
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doc/images/web_front_page.py
doc/images/wikimedia_bandedkrait.jpg
doc/images/wikimedia_cyl_ruffus.jpg
doc/images/gallery/gallery_big_pipeline.png
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doc/images/src/Backup_of_complex_file_dag.cdr
doc/images/src/Backup_of_complex_pipeline.cdr
doc/images/src/complex_conceptual.cdr
doc/images/src/complex_file_dag.cdr
doc/images/src/complex_pipeline.cdr
doc/images/src/key.cdr
doc/static_data/favicon32.ico
doc/static_data/ruffus.css
doc/static_data/ruffus.pdf
doc/static_data/small_logo.png
doc/static_data/example_scripts/complicated_example.py
doc/static_data/example_scripts/intermediate_example.py
doc/static_data/example_scripts/play_with_colours.py
doc/static_data/example_scripts/ruffus_template.py
doc/static_data/example_scripts/simpler.py
doc/tutorials/new_syntax.rst
doc/tutorials/new_syntax_worked_example.rst
doc/tutorials/new_syntax_worked_example_code.rst
doc/tutorials/new_tutorial/active_if.rst
doc/tutorials/new_tutorial/check_if_uptodate.rst
doc/tutorials/new_tutorial/checkpointing.rst
doc/tutorials/new_tutorial/checkpointing_code.rst
doc/tutorials/new_tutorial/combinatorics.rst
doc/tutorials/new_tutorial/combinatorics_code.rst
doc/tutorials/new_tutorial/command_line.rst
doc/tutorials/new_tutorial/decorators_compendium.rst
doc/tutorials/new_tutorial/dependencies.rst
doc/tutorials/new_tutorial/deprecated_files.rst
doc/tutorials/new_tutorial/deprecated_files_re.rst
doc/tutorials/new_tutorial/exceptions.rst
doc/tutorials/new_tutorial/flowchart_colours.rst
doc/tutorials/new_tutorial/flowchart_colours_code.rst
doc/tutorials/new_tutorial/inputs.rst
doc/tutorials/new_tutorial/inputs_code.rst
doc/tutorials/new_tutorial/introduction.rst
doc/tutorials/new_tutorial/introduction_code.rst
doc/tutorials/new_tutorial/list_of_ruffus_names.rst
doc/tutorials/new_tutorial/logging.rst
doc/tutorials/new_tutorial/logging_code.rst
doc/tutorials/new_tutorial/manual_chapter_numbers.inc
doc/tutorials/new_tutorial/manual_contents.rst
doc/tutorials/new_tutorial/merge.rst
doc/tutorials/new_tutorial/merge_code.rst
doc/tutorials/new_tutorial/mkdir.rst
doc/tutorials/new_tutorial/mkdir_code.rst
doc/tutorials/new_tutorial/multiprocessing.rst
doc/tutorials/new_tutorial/multiprocessing_code.rst
doc/tutorials/new_tutorial/onthefly.rst
doc/tutorials/new_tutorial/onthefly_code.rst
doc/tutorials/new_tutorial/originate.rst
doc/tutorials/new_tutorial/originate_code.rst
doc/tutorials/new_tutorial/output_file_names.rst
doc/tutorials/new_tutorial/output_file_names_code.rst
doc/tutorials/new_tutorial/parallel.rst
doc/tutorials/new_tutorial/pipeline_printout.rst
doc/tutorials/new_tutorial/pipeline_printout_code.rst
doc/tutorials/new_tutorial/pipeline_printout_graph.rst
doc/tutorials/new_tutorial/pipeline_printout_graph_code.rst
doc/tutorials/new_tutorial/posttask.rst
doc/tutorials/new_tutorial/split.rst
doc/tutorials/new_tutorial/split_code.rst
doc/tutorials/new_tutorial/subdivide_collate.rst
doc/tutorials/new_tutorial/subdivide_collate_code.rst
doc/tutorials/new_tutorial/transform.rst
doc/tutorials/new_tutorial/transform_code.rst
doc/tutorials/new_tutorial/transform_in_parallel.rst
doc/tutorials/new_tutorial/transform_in_parallel_code.rst
ruffus/__init__.py
ruffus/adjacent_pairs_iterate.py
ruffus/cmdline.py
ruffus/combinatorics.py
ruffus/dbdict.py
ruffus/drmaa_wrapper.py
ruffus/file_name_parameters.py
ruffus/graph.py
ruffus/parse_old_style_ruffus.py
ruffus/print_dependencies.py
ruffus/proxy_logger.py
ruffus/ruffus_exceptions.py
ruffus/ruffus_utility.py
ruffus/ruffus_version.py
ruffus/task.py
ruffus.egg-info/PKG-INFO
ruffus.egg-info/SOURCES.txt
ruffus.egg-info/dependency_links.txt
ruffus.egg-info/top_level.txt
ruffus/test/check_subpipeline_cmdline.py
ruffus/test/complicated_example.py
ruffus/test/create_test_script_from_dependency_tree.py
ruffus/test/draw_specified_dependency_tree.py
ruffus/test/five_second.py
ruffus/test/manual_test_ctrl_c_exceptions.py
ruffus/test/manual_test_ctrl_c_exceptions_drmaa.py
ruffus/test/manual_test_drmaa.py
ruffus/test/play_with_colours.py
ruffus/test/qrsh_workaround.py
ruffus/test/run_all_unit_tests.cmd
ruffus/test/run_all_unit_tests3.cmd
ruffus/test/simpler_with_shared_logging.py
ruffus/test/slow_process_for_testing.py
ruffus/test/test_N_x_M_and_collate.py
ruffus/test/test_active_if.py
ruffus/test/test_branching_dependencies.py
ruffus/test/test_check_if_uptodate.py
ruffus/test/test_cmdline.py
ruffus/test/test_collate.py
ruffus/test/test_combinatorics.py
ruffus/test/test_drmaa_wrapper_run_job_locally.py
ruffus/test/test_empty_files_decorator.py
ruffus/test/test_exceptions.py
ruffus/test/test_file_name_parameters.py
ruffus/test/test_files_decorator.py
ruffus/test/test_filesre_combine.py
ruffus/test/test_filesre_split_and_combine.py
ruffus/test/test_follows_mkdir.py
ruffus/test/test_functions_with_extras.py
ruffus/test/test_graphviz.py
ruffus/test/test_inputs_with_multiple_args_raising_exception.py
ruffus/test/test_job_completion_checksums.py
ruffus/test/test_job_history_with_exceptions.py
ruffus/test/test_mkdir.py
ruffus/test/test_newstyle_combinatorics.py
ruffus/test/test_newstyle_proxy.py
ruffus/test/test_newstyle_regex_error_messages.py
ruffus/test/test_pausing.py
ruffus/test/test_pipeline_printout_graph.py
ruffus/test/test_pool_manager.py
ruffus/test/test_posttask_merge.py
ruffus/test/test_proxy_logger.py
ruffus/test/test_regex_error_messages.py
ruffus/test/test_ruffus_utility.py
ruffus/test/test_ruffus_utility_parse_task_arguments.py
ruffus/test/test_runtime_data.py
ruffus/test/test_softlink_uptodate.py
ruffus/test/test_split_and_combine.py
ruffus/test/test_split_regex_and_collate.py
ruffus/test/test_split_subdivide_checkpointing.py
ruffus/test/test_subpipeline.py
ruffus/test/test_suffix_output_dir.py
ruffus/test/test_task_file_dependencies.py
ruffus/test/test_task_misc.py
ruffus/test/test_transform_add_inputs.py
ruffus/test/test_transform_formatter.py
ruffus/test/test_transform_inputs.py
ruffus/test/test_transform_with_no_re_matches.py
ruffus/test/test_tutorial7.py
ruffus/test/test_unicode_filenames.py
ruffus/test/test_verbosity.py
ruffus/test/test_with_logger.py