CHANGES.TXT
README.TXT
USAGE.TXT
ez_setup.py
setup.py
update.locally
doc/Makefile
doc/cheatsheet.rst
doc/conf.py
doc/contents.rst
doc/design.rst
doc/faq.rst
doc/gallery.rst
doc/global.inc
doc/glossary.rst
doc/history.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/task.rst
doc/todo.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/decorators/check_if_uptodate.rst
doc/decorators/collate.rst
doc/decorators/collate_ex.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/indicator_objects.rst
doc/decorators/jobs_limit.rst
doc/decorators/merge.rst
doc/decorators/parallel.rst
doc/decorators/posttask.rst
doc/decorators/split.rst
doc/decorators/split_ex.rst
doc/decorators/todo.sphinx
doc/decorators/transform.rst
doc/decorators/transform_ex.rst
doc/examples/bioinformatics/index.rst
doc/examples/bioinformatics/part1_code.rst
doc/examples/bioinformatics/part2.rst
doc/examples/bioinformatics/part2_code.rst
doc/examples/colour_schemes/flowchart_colours.rst
doc/examples/colour_schemes/flowchart_colours_code.rst
doc/images/colour_schemes.svg
doc/images/complete.svg
doc/images/complex_conceptual.jpg
doc/images/complex_file_dag.jpg
doc/images/complex_ruffus.jpg
doc/images/design.file_based_workflow.dot
doc/images/design.file_based_workflow.png
doc/images/design.task_based_workflow.dot
doc/images/design.task_based_workflow.png
doc/images/examples_bioinformatics_before.jpg
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
doc/images/examples_bioinformatics_transform.jpg
doc/images/flowchart_colour_schemes.png
doc/images/flowchart_colour_schemes.svg
doc/images/front_page_flowchart.png
doc/images/jobs_limit.png
doc/images/jobs_limit2.png
doc/images/logo.jpg
doc/images/manual_dependencies_flowchart.png.py
doc/images/manual_dependencies_flowchart1.dot
doc/images/manual_dependencies_flowchart1.png
doc/images/manual_dependencies_flowchart2.dot
doc/images/manual_dependencies_flowchart2.png
doc/images/manual_dependencies_flowchart3.dot
doc/images/manual_dependencies_flowchart3.png
doc/images/manual_dependencies_flowchart4.dot
doc/images/manual_dependencies_flowchart4.png
doc/images/manual_dependencies_flowchart_intro.png
doc/images/manual_dependencies_flowchart_intro.png.py
doc/images/manual_dependencies_flowchart_legend.dot
doc/images/manual_dependencies_flowchart_legend.png
doc/images/manual_exceptions.png
doc/images/manual_follows1.jpg
doc/images/manual_follows1.png
doc/images/manual_follows1.png.py
doc/images/manual_transform.png
doc/images/manual_transform_complex_outputs.png
doc/images/pretty_flowchart.png
doc/images/pretty_flowchart.png.py
doc/images/simple_tutorial_complex_flowchart.dot
doc/images/simple_tutorial_complex_flowchart.png
doc/images/simple_tutorial_complex_flowchart.py
doc/images/simple_tutorial_complex_flowchart_error.dot
doc/images/simple_tutorial_complex_flowchart_error.png
doc/images/simple_tutorial_complex_flowchart_error_with_key.png
doc/images/simple_tutorial_complex_flowchart_with_key.png
doc/images/simple_tutorial_decorator_syntax.png
doc/images/simple_tutorial_files1.png
doc/images/simple_tutorial_files2.png
doc/images/simple_tutorial_files3.png
doc/images/simple_tutorial_files4.png
doc/images/simple_tutorial_files5.png
doc/images/simple_tutorial_flowchart_legend.dot
doc/images/simple_tutorial_flowchart_legend.png
doc/images/simple_tutorial_follows.png
doc/images/simple_tutorial_hello_world.png
doc/images/simple_tutorial_hello_world_output.png
doc/images/simple_tutorial_intro_follows.png
doc/images/simple_tutorial_merge1.png
doc/images/simple_tutorial_merge2.png
doc/images/simple_tutorial_pipeline_printout1.png
doc/images/simple_tutorial_pipeline_printout2.png
doc/images/simple_tutorial_pipeline_printout3.png
doc/images/simple_tutorial_posttask.png
doc/images/simple_tutorial_split.png
doc/images/simple_tutorial_stage4_after.png
doc/images/simple_tutorial_stage4_before.png
doc/images/simple_tutorial_step3 copy.png
doc/images/simple_tutorial_step3.jpg
doc/images/simple_tutorial_step4.png
doc/images/simple_tutorial_step5.png
doc/images/simple_tutorial_step5_sans_key.png
doc/images/simple_tutorial_transform.png
doc/images/tutorial_complete.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/web_front_page.py
doc/images/wikimedia_cyl_ruffus.jpg
doc/images/gallery/gallery.big_pipeline.png
doc/images/gallery/gallery.big_pipeline.svg
doc/images/gallery/gallery.dless.png
doc/images/gallery/gallery.dless.py
doc/images/gallery/gallery.dless.svg
doc/images/gallery/gallery.rna_seq.png
doc/images/gallery/gallery.rna_seq.svg
doc/images/gallery/gallery.snp_annotation.png
doc/images/gallery/gallery.snp_annotation.svg
doc/images/gallery/gallery.snp_annotation_consequences.png
doc/images/gallery/gallery.snp_annotation_consequences.svg
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/play_with_colours.py
doc/static_data/example_scripts/simpler.py
doc/tutorials/manual/advanced_transform.rst
doc/tutorials/manual/chapter_numbers.inc
doc/tutorials/manual/check_if_uptodate.rst
doc/tutorials/manual/collate.rst
doc/tutorials/manual/dependencies.rst
doc/tutorials/manual/dependencies_code.rst
doc/tutorials/manual/exceptions.rst
doc/tutorials/manual/files.rst
doc/tutorials/manual/files_re.rst
doc/tutorials/manual/follows.rst
doc/tutorials/manual/jobs_limit.rst
doc/tutorials/manual/logging.rst
doc/tutorials/manual/logging_code.rst
doc/tutorials/manual/manual_code.rst
doc/tutorials/manual/manual_contents.rst
doc/tutorials/manual/manual_introduction.rst
doc/tutorials/manual/merge.rst
doc/tutorials/manual/onthefly.rst
doc/tutorials/manual/onthefly_code.rst
doc/tutorials/manual/parallel.rst
doc/tutorials/manual/parallel_processing.rst
doc/tutorials/manual/posttask.rst
doc/tutorials/manual/split.rst
doc/tutorials/manual/tasks_and_globs_in_inputs.rst
doc/tutorials/manual/tasks_as_recipes.rst
doc/tutorials/manual/tracing_pipeline_parameters.rst
doc/tutorials/manual/transform.rst
doc/tutorials/manual/transform_code.rst
doc/tutorials/simple_tutorial/simple_tutorial.rst
doc/tutorials/simple_tutorial/simple_tutorial_code.rst
doc/tutorials/simple_tutorial/step1_follows.rst
doc/tutorials/simple_tutorial/step2_files.rst
doc/tutorials/simple_tutorial/step2_files_code.rst
doc/tutorials/simple_tutorial/step3_run_pipeline.rst
doc/tutorials/simple_tutorial/step3_run_pipeline_code.rst
doc/tutorials/simple_tutorial/step4_run_pipeline_graphically.rst
doc/tutorials/simple_tutorial/step4_run_pipeline_graphically_code.rst
doc/tutorials/simple_tutorial/step5_split.rst
doc/tutorials/simple_tutorial/step5_split_code.rst
doc/tutorials/simple_tutorial/step6_transform.rst
doc/tutorials/simple_tutorial/step6_transform_code.rst
doc/tutorials/simple_tutorial/step7_merge.rst
doc/tutorials/simple_tutorial/step7_merge_code.rst
doc/tutorials/simple_tutorial/step8_posttask.rst
doc/tutorials/simple_tutorial/step8_posttask_code.rst
parameters/IGNORED_FILES
ruffus/__init__.py
ruffus/adjacent_pairs_iterate.py
ruffus/file_name_parameters.py
ruffus/graph.py
ruffus/print_dependencies.py
ruffus/proxy_logger.py
ruffus/re_glob.py
ruffus/ruffus_exceptions.py
ruffus/ruffus_utility.py
ruffus/ruffus_version.py
ruffus/svn-commit.tmp
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/complicated_example.py
ruffus/test/create_test_script_from_dependency_tree.py
ruffus/test/draw_specified_dependency_tree.py
ruffus/test/play_with_colours.py
ruffus/test/qrsh_workaround.py
ruffus/test/run_all_unit_tests.cmd
ruffus/test/simpler.py
ruffus/test/simpler_at_runtime.py
ruffus/test/simpler_with_shared_logging.py
ruffus/test/test_N_x_M_and_collate.py
ruffus/test/test_branching_dependencies.py
ruffus/test/test_collate.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_files_post_merge.py
ruffus/test/test_filesre_combine.py
ruffus/test/test_filesre_split_and_combine.py
ruffus/test/test_follows_mkdir.py
ruffus/test/test_inputs_with_multiple_args_raising_exception.py
ruffus/test/test_pausing.py
ruffus/test/test_ruffus_utility.py
ruffus/test/test_script.py_template
ruffus/test/test_split_and_combine.py
ruffus/test/test_split_regex_and_collate.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_inputs.py
ruffus/test/test_transform_with_no_re_matches.py
ruffus/test/test_tutorial7.py
ruffus/test/test_unicode_filenames.py
ruffus/test/auto_generated_pipeline_examples/parallel.py
ruffus/test/auto_generated_pipeline_examples/simple.py
ruffus/test/auto_generated_pipeline_examples/simpler.py
ruffus/test/data_for_complicated_example/all_genes_in_each_species/fly.genes.fa
ruffus/test/data_for_complicated_example/all_genes_in_each_species/octopus.genes.fa
ruffus/test/data_for_complicated_example/all_genes_in_each_species/spider.genes.fa
ruffus/test/data_for_complicated_example/all_genes_in_each_species/worm.genes.fa
ruffus/test/data_for_complicated_example/unknown_genes/gene_sets1.genes.fa
ruffus/test/data_for_complicated_example/unknown_genes/gene_sets2.genes.fa
ruffus/test/dependency_data/dag.dependency
ruffus/test/dependency_data/non_dag.dependency
ruffus/test/dependency_data/simple.dag
ruffus/test/dependency_data/simpler.dag