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ruffus contents manual introduction installation latest changes new object orientated syntax worked example for new object orientated syntax for ruffus in version 2.6 python code for: new object orientated syntax for ruffus in version 2.6 future plans faq hall of fame who is ruffus ? manual chapter 1 : an introduction to basic ruffus syntax chapter 2 : transforming data in a pipeline with @transform chapter 3 : more on @transform -ing data chapter 4 : creating files with @originate chapter 5 : understanding how your pipeline works with pipeline_printout(...) chapter 6 : running ruffus from the command line with ruffus.cmdline chapter 7 : displaying the pipeline visually with pipeline_printout_graph(...) chapter 8 : specifying output file names with formatter() and regex() chapter 9 : preparing directories for output with @mkdir() chapter 10 : checkpointing: interrupted pipelines and exceptions chapter 11 : pipeline topologies and a compendium of ruffus decorators chapter 12 : splitting up large tasks / files with @split chapter 13 : @merge multiple input into a single result chapter 14 : multiprocessing, drmaa and computation clusters chapter 15 : logging progress through a pipeline chapter 16 : @subdivide tasks to run efficiently and regroup with @collate chapter 17 : @combinations , @permutations and all versus all @product chapter 18 : turning parts of the pipeline on and off at runtime with @active_if chapter 19 : signal the completion of each stage of our pipeline with @posttask chapter 20 : manipulating task inputs via string substitution using inputs() and add_inputs() chapter 21 : esoteric: generating parameters on the fly with @files chapter 22 : esoteric: running jobs in parallel without files using @parallel chapter 23 : esoteric: writing custom functions to decide which jobs are up to date with @check_if_uptodate appendix 1 : flow chart colours with pipeline_printout_graph(...) appendix 2 : how dependency is checked appendix 3 : exceptions thrown inside pipelines appendix 4 : names exported from ruffus appendix 5 : @files : deprecated syntax appendix 6 : @files_re : deprecated syntax using regular expressions chapter 1 : python code for an introduction to basic ruffus syntax chapter 1 : python code for transforming data in a pipeline with @transform chapter 3 : python code for more on @transform -ing data chapter 4 : python code for creating files with @originate chapter 5 : python code for understanding how your pipeline works with pipeline_printout(...) chapter 7 : python code for displaying the pipeline visually with pipeline_printout_graph(...) chapter 8 : python code for specifying output file names with formatter() and regex() chapter 9 : python code for preparing directories for output with @mkdir() chapter 10 : python code for checkpointing: interrupted pipelines and exceptions chapter 12 : python code for splitting up large tasks / files with @split chapter 13 : python code for @merge multiple input into a single result chapter 14 : python code for multiprocessing, drmaa and computation clusters chapter 15 : python code for logging progress through a pipeline chapter 16 : python code for @subdivide tasks to run efficiently and regroup with @collate chapter 17 : python code for @combinations , @permutations and all versus all @product chapter 20 : python code for manipulating task inputs via string substitution using inputs() and add_inputs() chapter 21 : esoteric: python code for generating parameters on the fly with @files appendix 1 : python code for flow chart colours with pipeline_printout_graph(...) construction of a simple pipeline to run blast jobs part 2: a slightly more practical pipeline to run blasts jobs ruffus code ruffus code example code for faq good practices: "what is the best way of handling data in file pairs (or triplets etc.)?" reference ruffus functions pipeline_run pipeline_printout pipeline_printout_graph pipeline_get_task_names run_job ruffus decorators originate split transform merge subdivide transform collate graphviz mkdir jobs_limit posttask active_if follows product permutations combinations combinations_with_replacement parameters on the fly with @files check_if_uptodate parallel files @files_re core combinatorics advanced esoteric! indicator objects formatter suffix regex add_inputs inputs mkdir touch_file output_from combine design & architecture gnu make scons , rake and other make alternatives managing pipelines stage-by-stage using ruffus alternatives to ruffus implementation tips release blogger dbdict.py how to write new decorators implementation notes ctrl-c handling python3 compatability refactoring: parameter handling formatter @product() @permutations(...), @combinations(...), @combinations_with_replacement(...) drmaa alternatives task completion monitoring @mkdir(...), parameter handling add object orientated interface cheat sheet 1. annotate functions with ruffus decorators 2. print dependency graph if necessary 3. run the pipeline glossary ruffus.task decorators pipeline functions logging implementation: exceptions and errors ruffus.proxy_logger create proxy for logging for use with multiprocessing proxies for a log: create a logging object ruffus docs » ruffus is a computation pipeline library for python. it is open-sourced, powerful and user-friendly, and widely used in science and bioinformatics. citation: please cite ruffus as: leo goodstadt (2010) : ruffus: a lightweight python library for computational pipelines. bioinformatics 26(21): 2778-2779 welcome ruffus is designed to allow scientific and other analyses to be automated with the minimum of fuss and the least effort. these are ruffus 's strengths: lightweight : suitable for the simplest of tasks scalable : handles even fiendishly complicated pipelines which would cause make or scons to go cross-eyed and recursive. standard python : no "clever magic", no pre-processing. unintrusive : unambitious, lightweight syntax which tries to do this one small thing well. please join me (email: ruffus_lib at llew.org.uk) in setting the direction of this project if you are interested. documentation download to install ruffus simple tutorial start here for a quick introduction to ruffus manual (pdf) for an-depth demonstration of all ruffus features table of contents for an complete listing of all the documentation frequently answered questions for any common problems, clever solutions from the community design to understand the design of ruffus cheat sheet for ruffus syntax get ruffus ruffus is available as an easy-install able package on the python package index . just run: sudo pip install ruffus --upgrade or easy_install -u ruffus the very latest (in development) code can be obtained via git : git clone https://[email protected]/p/ruffus/ feedback and getting involved: the ruffus project is hosted with google code here. subscribe to the ruffus_discuss mailing list email: check out the mailing list without subscribing here. bugs or feature requests can be posted here. © copyright 2009-2015 leo goodstadt. built with sphinx .

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http://www.ruffus.org.uk/implementation_notes.html
http://www.ruffus.org.uk/task.html#implementation
http://www.ruffus.org.uk/implementation_notes.html#release
http://www.ruffus.org.uk/proxy_logger.html#proxies-for-a-log
http://www.ruffus.org.uk/implementation_notes.html#permutations-combinations-combinations-with-replacement
http://www.ruffus.org.uk/history.html
http://www.ruffus.org.uk/tutorials/new_tutorial/mkdir_code.html
http://www.ruffus.org.uk/installation.html
http://www.ruffus.org.uk/examples/bioinformatics/part2.html
http://www.ruffus.org.uk/tutorials/new_tutorial/dependencies.html
http://www.ruffus.org.uk/tutorials/new_tutorial/deprecated_files_re.html
http://www.ruffus.org.uk/decorators/decorators.html#advanced
http://www.ruffus.org.uk/pipeline_functions.html#index-1
http://www.ruffus.org.uk/decorators/posttask.html
http://www.ruffus.org.uk/examples/bioinformatics/index.html

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