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SmileTrain

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Python requirements

SmileTrain is developed against Python 2.7.3.

Documentation

Documents in the github wiki (in the right-hand panel). A (possibly old) copy is in the doc/ folder.

Scripts are annotated with docstrings that can be read using pydoc. To view documentation for script.py, run pydoc script.

Tests

Unit tests are in the test folder. You can run the tests from the top directory by running python -m unittest discover.

Usage

  • Enter your user information in the config file before use.
  • Make sure your .bash_rc loads python 2.7. Otherwise, argparse will die. At the start of my .bash_rc, I have
    • source /etc/profile.d/modules.sh
    • module add python/2.7.3
  • Run the tests.
  • Run otu_caller.py with the command line option --dry_run before you actually submit any jobs. Check that the output commands look like what you actually want to submit to the cluster!