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LICENSE

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+Use or reproduction of these materials, in whole or in part, by any non-academic organization whether or not for non-commercial (including research) or commercial purposes is prohibited, except with written permission of McMaster University. Commercial uses are offered only pursuant to a written license and user fee. To obtain permission and begin the licensing process, see http://card.mcmaster.ca/about.

README.rst

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+Resistance Gene Identifier (RGI) 
+--------------------------------------------
+
+This application is used to predict resistome(s) from protein or nucleotide data based on homology and SNP models. The application uses data from `CARD database <https://card.mcmaster.ca/>`_.
+
+Table of Contents
+-------------------------------------
+
+- `License`_
+- `Requirements`_
+- `Install Dependecies`_
+- `Install RGI from project root`_
+- `Running RGI Tests`_
+- `Running RGI`_
+- `Usage`_
+- `Support & Bug Reports`_
+
+License
+--------
+Use or reproduction of these materials, in whole or in part, by any non-academic organization whether or not for non-commercial (including research) or commercial purposes is prohibited, except with written permission of McMaster University. Commercial uses are offered only pursuant to a written license and user fee. To obtain permission and begin the licensing process, see `CARD website <https://card.mcmaster.ca/about>`_
+
+Requirements
+--------------------
+
+- `Prodigal v2.6.3 <https://github.com/hyattpd/prodigal/wiki/Installation>`_
+- `NCBI BLAST v2.6.0+ <https://blast.ncbi.nlm.nih.gov/Blast.cgi>`_
+- `DIAMOND v0.8.36 <https://ab.inf.uni-tuebingen.de/software/diamond>`_
+- `Python 3.6 <https://www.python.org/>`_
+
+Install Dependecies
+--------------------
+
+- pip3 install numpy
+- pip3 install biopython
+- pip3 install profilehooks
+- pip3 install filetype
+- pip3 install psycopg2
+- pip3 install pandas
+
+Install RGI from project root
+-----------------------------
+
+- pip3 install .
+
+
+Running RGI Tests
+-------------------
+
+- cd tests
+- pytest -v
+
+Running RGI
+-------------------
+
+- rgi -h
+
+Usage
+-------------------
+
+.. code-block:: sh
+
+   usage: rgi <command> [<args>] 
+            commands are:
+               main    Runs rgi application
+               tab     Creates a Tab-delimited from rgi results
+               parser  Creates categorical .json files RGI wheel visualization. An input .json file containing the RGI results must be input.
+               load    Loads CARD database json file
+               clean   Removes BLAST databases and temporary files
+               galaxy  Galaxy project wrapper
+
+   Resistance Gene Identifier - 4.0.0
+
+   positional arguments:
+   command     Subcommand to run
+
+   optional arguments:
+   -h, --help  show this help message and exit
+
+   Use the Resistance Gene Identifier to predict resistome(s) from protein or
+   nucleotide data based on homology and SNP models. Check
+   https://card.mcmaster.ca/download for software and data updates. Receive email
+   notification of monthly CARD updates via the CARD Mailing List
+   (https://mailman.mcmaster.ca/mailman/listinfo/card-l)
+
+
+Support & Bug Reports
+----------------------
+
+Please log an issue on `github issue <https://github.com/arpcard/oop/issues>`_.
+
+You can email the CARD curators or developers directly at `[email protected] <mailto:[email protected]>`_, via Twitter at `@arpcard <http://www.twitter.com/arpcard>`_.
+