
# Instructions for use:
# 1. Open this script in a text editor or IDE. Support for Python
#    syntax highlighting is helpful.
# 2. Search or scan visually for '<' or '>' characters to find places where
#    user input (e.g. a filepath or column name) is required. If syntax
#    highlighting is enabled, '<' and '>' will appear as syntax errors.
# 3. Search for 'FIXME' comments in the script, and respond as directed.
# 4. Remove all 'FIXME' comments from the script completely. Failure to do so
#    may result in 'Missing Option' errors
# 5. Adjust the arguments to the commands below to suit your data and metadata.
#    If your data is not identical to that in the replayed analysis,
#    changes may be required. (e.g. sample ids or rarefaction depth)
# 6. Optional: search for 'SAVE' comments in the script, commenting out the
#    `some_result.save` lines for any Results you do not want saved to disk.
# 7. Activate your replay conda environment, and confirm you have installed all
#    plugins used by the script.
# 8. Run this script with `python <path to this script>`, or paste commands
#    into a python interpreter or jupyter notebook for an interactive analysis