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A Python pipeline management system
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pyleaf
samples
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CHANGES.txt
COPYING.txt
MANIFEST.in
README.md
README.txt
setup.py

README.md

pyleaf README

pyleaf is the Python implementation of the Leaf system. The Leaf system is a pipeline (AKA data flow or data analysis protocol) management system that allows to design the pipeline as an ASCII-art diagram through a language called LGL (Leaf Graph Language, see https://github.com/franapoli/lglc - also see INSTALL paragraph below).

Scientific publications

Please consider the reference below to cite Leaf if you are using it. The paper is also a good introductory guide.

Napolitano, F., Mariani-Costantini, R., Tagliaferri, R., 2013. Bioinformatic pipelines in Python with Leaf. BMC Bioinformatics 14, 201.

Features

  • Thin, lightweight, code-independent Abstraction Layer.
  • Data flow graph embedded directly into Python source code.
  • Automatic creation and management of variables associated with node outputs.
  • Automatic persistent storage and retrieval of node outputs.
  • Session persistence (i.e. run half project, reboot machine, automatically start again from the last processed node).
  • Lazy builds (avoid running nodes that are not necessary for the build of a requested resource).
  • Multiprocessing (independent nodes run in parallel).
  • Enforcement of code version consistency between nodes (i.e. automatically reprocess all nodes deriving from node A if node A is found to be changed).
  • Automatic time and space requirements statistics.
  • Automatic publishing (producing hypertext with visual representation of the protocol, processing statistics, link to node outputs, node documentation and source code).

pipeline example

          / regression -> plots [F]
getData  <
          \  / @plots
           .<
             \ exportCSV [F]

Home Page

   http://www.francesconapolitano.it/leaf

INSTALL

pyleaf requires lglc. Precompiled Windows and Linux binaries are available at:

http://www.francesconapolitano.it/leaf/downloads

C++ sources from:

https://github.com/franapoli/lglc

To install pyleaf:

python setup.py install

You may require administrator rights.

Using pyleaf

Please check the "doc" directory (if this is part of a source distribution you may need to build the documentation, see "site_and_doc" directory). You may also want to start with the tutorial "ex1_tut.txt" in the directory "samples".

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