|--------------------------------------------------------------------------
| Running RGI localy
|--------------------------------------------------------------------------


|--------------------------------------------------------------------------
| Files
|--------------------------------------------------------------------------


`-- rgi/
   |-- _data/
         |-- card.json
   |-- _db/
         ... (BLAST DBs)
   |-- _docs/
         |-- INSTALL
         |-- README
   |-- _tmp/
   |-- tests/
   |-- __init__.py
   |-- blastnsnp.py
   |-- clean.py
   |-- contigToORF.py
   |-- contigToProteins.py
   |-- convertJsonToTSV.py
   |-- create_gff3_file.py
   |-- filepaths.py
   |-- formatJson.py
   |-- fqToFsa.py
   |-- load.py
   |-- rgi.py
   |-- rrna.py
   


|--------------------------------------------------------------------------
| Commands for Running RGI localy
|--------------------------------------------------------------------------


$ python rgi.py -h

$ python clean.py -h

$ python convertJsonToTSV.py -h

$ python load.py -h

$ python formatJson.py -h 


|--------------------------------------------------------------------------
| Running RGI system-wide
|--------------------------------------------------------------------------

# install RGI

$ conda install --channel rgi

# un-install RGI

$ conda remove --channel rgi

|--------------------------------------------------------------------------
| Commands for Running RGI system-wide
|--------------------------------------------------------------------------

$ rgi -h

$ rgi_clean -h

$ rgi_jsontab -h

$ rgi_load -h

$ rgi_jsonformat -h

