Testing Make_KO for Windows

[mattfio]

Notes from running through the process document "Building_a_CPIC_KO.md" on a Windows 10 OS - Matt Fiorillo and Koki.

Overall:

• Ensure user has Bash installed! Instructions found here: https://www.howtogeek.com/249966/how-to-install-and-use-the-linux-bash-shell-on-windows-10/
• Need to make sure user has both python versions installed: Python (pip) and Python 3 (pip).
  --- Ran into trouble getting correct version installed and then updating each. Instructions came in error messagc in bash
  --- Also need to install xlrd
• Perhaps explain that users can download files by opening file in GitHub, clicking Raw, copy the code text, open a notepad file in the appropriate directly, then paste in code and save using appropriate (usually same) filename.

Building a CPIC KO:

• To the existing list, add that user should download the excel_to_dictionary .py and the skeleton_geno_pheno-bas

Converting table

• Ensure that user saves all files into the same directory as the excel tables
• for Kb implementation client #4 clarify that only the filename (no path) is needed
• dictionary file gets saved with ".xlsx.txt" - minor thing but hopefully can remove the ".xlsx"

Creating kog.json

• for #5, swapping in a filepath, clarify that Windows format filepath can be used

Creating metadata.json

• Kb implementation2 #3 - include recommendations about KO titles in instructions?
• #5 - add clarification about which function name to select from the payload. i.e. in "skeleton_geno_pheno-base.py" the "alleleFormat" function shows first, but "getPhenotype" is the one you want to use. Not clear to all users.
• Also #5 - clarify about not including parameter. i.e. using " getPhenotype" and not " getPhenotype(geno)"

Building the KO

• could not get build.py to work using these steps. build.py uses python2 - could be source of issue