File	Date	Author	Commit
data	2017-05-10	yye	[2843fc] add an output file *.html.txt, similar to the h...
tests	2016-04-13	yye	[716991] initial commit
tools	2016-04-25	yye	[9a691b] upldate FragGeneScan
README	2016-04-25	yye	[ca7cef] update README
fun4me.py	2017-05-10	yye	[055ab5] add an output file *.html.txt, similar to the h...
install	2016-06-14	yye	[d84ec4] revised fun4me.py & install

Read Me

Package Name: Fun4Me (Functional Annotation for Metagenomics)

Developers: Yuzhen Ye <yye@indiana.edu> and Fatemeh Sharifi <fsharifi@umail.iu.edu>
Affiliation: School of Informatics and Computing, Indiana University, Bloomington

The development of Fun4Me was supported by NIH grant 1R01HG004908 &  NSF grant DBI-0845685.

Fun4Me is free software under the terms of the GNU General Public License as published by
the Free Software Foundation.

Introduction
==================

Structure of this package
==================
install -- a bash script for installation
data -- a folder for important data
tools -- a place where the tools (FragGeneScan, RAPSearch & MinPath) go
tests -- a folder where you can find a small metagenomic dataset for testing
fun4me.py -- the wrapper script for one-stop application of this package

Installation
==================
./install

Preprocessing similarity search database
==================
cd data
../tools/RAPSearch2.23_64bits/bin/prerapsearch -d uniref90-go-noE.fasta -n uniref90-go-noE.rap

(This is a slow process; please be patient. This preprocessing step only needs to be done once)

Testing the programs
==================
cd tests
../fun4me.py -i SRS011061-reads-small.fa -o SRS011061-reads-small

Running the programs
==================
./fun4me.py