[Biopython-dev] A workflow management module for BioPython.

Bo Peng ben.bob at gmail.com
Wed Mar 11 12:45:05 UTC 2015

Dear BioPython developers,

There has been dozens of workflow management systems but most of them
require users to learn a new system and even a new language. Because of the
strong need to convert shell commands to pipelines with advanced execution
features, we have developed a light-weight bioinformatics pipeline system
with emphasis on readability and sharing. The system uses .ini format for
pipeline specification (in comparison to XML format used by many other
systems such as galaxy) and specifies the core of pipelines (actions and
file flow) in a highly condensed and readable way. This makes it easier for
users to share pipelines with collaborators, adapt them to local running
environment, and update them for newer versions of tools and annotation
sources. The system uses a number of Python features in its pipeline
specification system (e.g. use of python expressions and lambda functions)
and uses Python for user-defined actions.

This tool has been developed and used by the variant tools community for a
while (tentatively named VPT,
http://varianttools.sourceforge.net/Pipeline/HomePage, with features
described in a powerpoint presentation on its home page). As a general
pipeline management tool that has been applied to many other areas such as
RNA seq data analysis, VPT does not really belong to variant tools so we
are thinking of moving it out of variant tools. Because BioPython does not
currently provide such a module, I am writing to see if there is any
interest in merging VPT to BioPython. It would most likely be a complete
re-design and re-implementation after incorporating your ideas but we are
willing to contribute the code to BioPython if you consider it as a
valuable addition to BioPython. In addition to the existing features, I am
thinking of actions that make use of BioPython's ability to query
databases, and functions to convert VPT pipelines to other systems such as
Galaxy and Taverna.

Thank you very much for your attention and please feel free to let me know
if you have any question or suggestion. If you are wondering about my
qualification, I am the author of a Python-based population genetics
simulation program simuPOP and had a long history of contributing to open
source projects such as the LyX project (former core developer).

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