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Workflow Python Manager for Reproducible Science

Project description

WopMars is a database-driven workflow manager written in python similar to GNU Makefile or Snakemake. The difference is that the definition file of WopMars takes into account input/output SQLITE table defined as python paths to SQLAlchemy models.

You can install the latest WopMars version via “pypi”:

pip install wopmars

Run a quick example:

wopmars example
cd example
pip install -e .
wopmars -D sqlite:///db.sqlite -w Wopfile.yml -v

If there were not errors, you can look at the content of the sqlite db.

$ sqlite3 db.sqlite '.tables'

Piece                            wom_TableInputOutputInformation
PieceCar                         wom_TableModificationTime
wom_Execution                    wom_ToolWrapper
wom_FileInputOutputInformation   wom_TypeInputOrOutput

$ sqlite3 db.sqlite "select * from Piece limit 5"


The WopMars documentation with user guide and API reference is hosted at Read The Docs.

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