CHANGES.TXT
README.TXT
USAGE.TXT
ez_setup.py
ez_setup.pyc
setup.py
doc/Makefile
doc/cheatsheet.rst
doc/conf.py
doc/contents.rst
doc/history.rst
doc/make.bat
doc/propset
doc/proxy_logger.rst
doc/task.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
doc/complex_dags/jpg/task17_from_task9_sm.jpg
doc/complex_dags/jpg/task17_sm.jpg
doc/complex_dags/jpg/task25_from_task9.jpg
doc/complex_dags/jpg/task25_from_task9_sm.jpg
doc/complex_dags/png/all.png
doc/complex_dags/png/non_dag.png
doc/complex_dags/png/task17.png
doc/complex_dags/png/task17_from_task9.png
doc/complex_dags/png/task25_from_task9.png
doc/complex_dags/svg/all.svg
doc/complex_dags/svg/non_dag.svg
doc/complex_dags/svg/task17.svg
doc/complex_dags/svg/task17_from_task9.svg
doc/complex_dags/svg/task25_from_task9.svg
doc/example_scripts/complicated_example.py
doc/example_scripts/intermediate_example.py
doc/example_scripts/simpler.py
doc/example_scripts/simpler_with_shared_logging.py
doc/images/complete.svg
doc/images/complex_conceptual.jpg
doc/images/complex_file_dag.jpg
doc/images/complex_ruffus.jpg
doc/images/logo.jpg
doc/images/tutorial_complete.jpg
doc/images/tutorial_flowchart_ex1.jpg
doc/images/tutorial_force_from_task1.jpg
doc/images/tutorial_four_stage_pipeline.jpg
doc/images/tutorial_key.jpg
doc/images/tutorial_maximal_mode.jpg
doc/images/tutorial_minimal_mode.jpg
doc/images/tutorial_pipeline_key.jpg
doc/images/wikimedia_cyl_ruffus.jpg
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/ruffus.css
doc/static_data/example_scripts/complicated_example.py
doc/static_data/example_scripts/intermediate_example.py
doc/static_data/example_scripts/simpler.py
parameters/IGNORED_FILES
ruffus.egg-info/PKG-INFO
ruffus.egg-info/SOURCES.txt
ruffus.egg-info/dependency_links.txt
ruffus.egg-info/top_level.txt
src/ruffus/__init__.py
src/ruffus/adjacent_pairs_iterate.py
src/ruffus/file_name_parameters.py
src/ruffus/graph.py
src/ruffus/print_dependencies.py
src/ruffus/proxy_logger.py
src/ruffus/ruffus_exceptions.py
src/ruffus/ruffus_utility.py
src/ruffus/ruffus_version.py
src/ruffus/svn-commit.tmp
src/ruffus/task.py
src/ruffus/test/complicated_example.py
src/ruffus/test/create_test_script_from_dependency_tree.py
src/ruffus/test/draw_specified_dependency_tree.py
src/ruffus/test/qrsh_workaround.py
src/ruffus/test/simpler.py
src/ruffus/test/simpler_with_shared_logging.py
src/ruffus/test/test_branching_dependencies.py
src/ruffus/test/test_exceptions.py
src/ruffus/test/test_filesre_combine.py
src/ruffus/test/test_filesre_split_and_combine.py
src/ruffus/test/test_follows_mkdir.py
src/ruffus/test/test_script.py_template
src/ruffus/test/test_task_file_dependencies.py
src/ruffus/test/test_task_misc.py
src/ruffus/test/test_task_param_factory.py
src/ruffus/test/auto_generated_pipeline_examples/parallel.py
src/ruffus/test/auto_generated_pipeline_examples/simple.py
src/ruffus/test/auto_generated_pipeline_examples/simpler.py
src/ruffus/test/data_for_complicated_example/all_genes_in_each_species/fly.genes.fa
src/ruffus/test/data_for_complicated_example/all_genes_in_each_species/octopus.genes.fa
src/ruffus/test/data_for_complicated_example/all_genes_in_each_species/spider.genes.fa
src/ruffus/test/data_for_complicated_example/all_genes_in_each_species/worm.genes.fa
src/ruffus/test/data_for_complicated_example/unknown_genes/gene_sets1.genes.fa
src/ruffus/test/data_for_complicated_example/unknown_genes/gene_sets2.genes.fa
src/ruffus/test/dependency_data/dag.dependency
src/ruffus/test/dependency_data/non_dag.dependency
src/ruffus/test/dependency_data/simple.dag
src/ruffus/test/dependency_data/simpler.dag
src/ruffus/test/qrsh_workaround/output.1
src/ruffus/test/qrsh_workaround/output.10
src/ruffus/test/qrsh_workaround/output.2
src/ruffus/test/qrsh_workaround/output.3
src/ruffus/test/qrsh_workaround/output.4
src/ruffus/test/qrsh_workaround/output.5
src/ruffus/test/qrsh_workaround/output.6
src/ruffus/test/qrsh_workaround/output.7
src/ruffus/test/qrsh_workaround/output.8
src/ruffus/test/qrsh_workaround/output.9