CHANGES.TXT
README.TXT
USAGE.TXT
ez_setup.py
ez_setup.pyc
ruffus_version.py
setup.py
doc/Design.rst
doc/FAQ.rst
doc/Glossary.rst
doc/Introduction.rst
doc/Makefile
doc/Todo.rst
doc/Tutorial.rst
doc/cheatsheet.rst
doc/complicated_example.rst
doc/complicated_example_code.rst
doc/conf.py
doc/contents.rst
doc/intermediate_example.rst
doc/intermediate_example_code.rst
doc/make.bat
doc/propset
doc/sharing_data_across_jobs_example.rst
doc/sharing_data_across_jobs_example_code.rst
doc/simple_tutorial.rst
doc/simpler.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/html/.buildinfo
doc/html/Design.html
doc/html/FAQ.html
doc/html/Glossary.html
doc/html/Introduction.html
doc/html/Overview.html
doc/html/Todo.html
doc/html/Tutorial.html
doc/html/cheatsheet.html
doc/html/complicated_example.html
doc/html/complicated_example_code.html
doc/html/contents.html
doc/html/genindex.html
doc/html/index.html
doc/html/intermediate_example.html
doc/html/intermediate_example_code.html
doc/html/modindex.html
doc/html/objects.inv
doc/html/search.html
doc/html/searchindex.js
doc/html/sharing_data_across_jobs_example.html
doc/html/sharing_data_across_jobs_example_code.html
doc/html/simple_tutorial.html
doc/html/simpler.html
doc/html/task.html
doc/html/_images/complete.jpg
doc/html/_images/complex_conceptual.jpg
doc/html/_images/complex_file_dag.jpg
doc/html/_images/complex_pypaline.jpg
doc/html/_images/complex_ruffus.jpg
doc/html/_images/cyl_ruffus.jpg
doc/html/_images/force_from_task1.jpg
doc/html/_images/four_stage_pipeline.jpg
doc/html/_images/key.jpg
doc/html/_images/maximal_mode.jpg
doc/html/_images/minimal_mode.jpg
doc/html/_sources/Design.txt
doc/html/_sources/FAQ.txt
doc/html/_sources/Glossary.txt
doc/html/_sources/Introduction.txt
doc/html/_sources/Overview.txt
doc/html/_sources/Todo.txt
doc/html/_sources/Tutorial.txt
doc/html/_sources/cheatsheet.txt
doc/html/_sources/complicated_example.txt
doc/html/_sources/complicated_example_code.txt
doc/html/_sources/contents.txt
doc/html/_sources/index.txt
doc/html/_sources/intermediate_example.txt
doc/html/_sources/intermediate_example_code.txt
doc/html/_sources/sharing_data_across_jobs_example.txt
doc/html/_sources/sharing_data_across_jobs_example_code.txt
doc/html/_sources/simple_tutorial.txt
doc/html/_sources/simpler.txt
doc/html/_sources/task.txt
doc/html/_static/basic.css
doc/html/_static/contents.png
doc/html/_static/default.css
doc/html/_static/doctools.js
doc/html/_static/file.png
doc/html/_static/jquery.js
doc/html/_static/logo.jpg
doc/html/_static/minus.png
doc/html/_static/navigation.png
doc/html/_static/plus.png
doc/html/_static/pygments.css
doc/html/_static/pypaline.css
doc/html/_static/ruffus.css
doc/html/_static/searchtools.js
doc/html/_static/sphinxdoc.css
doc/html/_static/example_scripts/complicated_example.py
doc/html/_static/example_scripts/intermediate_example.py
doc/html/_static/example_scripts/simpler.py
doc/html/_static/example_scripts/simpler_with_shared_logging.py
doc/images/complete.jpg
doc/images/complete.svg
doc/images/complex_conceptual.jpg
doc/images/complex_file_dag.jpg
doc/images/complex_ruffus.jpg
doc/images/cyl_ruffus.jpg
doc/images/force_from_task1.jpg
doc/images/four_stage_pipeline.jpg
doc/images/key.jpg
doc/images/logo.jpg
doc/images/maximal_mode.jpg
doc/images/minimal_mode.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/requires.txt
ruffus.egg-info/top_level.txt
src/ruffus_version.py
src/ruffus/__init__.py
src/ruffus/adjacent_pairs_iterate.py
src/ruffus/graph.py
src/ruffus/print_dependencies.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/intermediate_example.py
src/ruffus/test/qrsh_workaround.py
src/ruffus/test/simpler.py
src/ruffus/test/simpler_with_shared_logging.py
src/ruffus/test/test_exceptions.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/data_for_intermediate_example/genes/001.gene
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