5. More info

Recommended reading

• Unix shell background info here, here, here, and here.
• GNU Bash Reference Manual

Developer information

DONE

• Fix homebrew formula to automatically set up piranha executable and source completions functions. DONE! ✅
• Add dynamic tab completion for function names. DONE! ✅
• Improve option and usage sections of BEASTRunner function. DONE! :white_heck_mark:
• Add MrBayes functions. DONE! ✅
• Add options to MrBayesPostProc function, e.g. for burnin frac and stepping-stone MLE analysis. DONE! ✅

DONE

• Change phylipSubsampler function so that it accounts for missing data (currently does not).
• Give supercomputer scripts options (header w/flags) that will work for both a) TORQUE/PBS and b) SLURM Workload Manager cluster management and job scheduling systems (need meticulous work on this in Super-pyRAD2PartitionFinder, BEASTRunner, BEASTPostProc, and RAxMLRunner.sh)
• Add mrbayes and beast model options to pyrad2PartitionFinder and supercomputer version of the same script.
• Make pyrad and ipyrad batch run scripts available
• Consider separate functions to work with ipyrad
• Add capacity of adding or not adding path sampling/stepping-stone sampling to BEAST runs (use BEASTRunner as springboard to develop tools in BEAST_PathSampling dir)

December 9, 2020 - Justin C. Bagley, Jacksonville, AL, USA

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