Overview

NOTE => This script has been deprecated. Use loc_files.

There are 2 scripts:
    1. create_loc.py - A script to generate .loc files from Galaxy main's rsynced indexes folder.
       
    2. create_2bit_to_fa.py - A script to convert .2bit files to .fa in 'dbkey/seq/' folders
       because the rync from galaxy main's datacache ommited fasta's to save our bandwith:
       http://wiki.g2.bx.psu.edu/Admin/Data%20Integration 
       
       Requires twoBitToFa
       Where to download:
           http://genome.ucsc.edu/FAQ/FAQlicense#license3
           http://genome-source.cse.ucsc.edu/gitweb/?p=kent.git;a=summary
           git clone git://genome-source.cse.ucsc.edu/kent.git

Important points for creating loc:
    - Assumed folder structure is GENOMES_DIR/dbkey/tool_index_dir/<...dir structure depending on tool...>
    - ucsc's build.txt : 
        Currently: Every dbkey in GENOMES_DIR will be cross checked and ignored if not found in build.txt

Procedure to add support for a tool:
1. Add an entry into tool_data_table_conf.xml
2. Add an entry to TOOLS in create_loc.py
    - Add the tool name and the name of the folder that will be associated with that tool in the indexes folder
3. Write a manager for the tool in tool_managers.py
    - Try to reuse code by either using python inheritance to 
        inherit a generic manager or 
        write a new generic manager 


Supported tool list (more to be added):
all_fasta
bowtie
bowtie color (only full no variants)
bwa (only full no variants)
bwa color (only full no variants)
codingSnps
gatk
lastz
mosaik
ngs_sim
picard
sam
sequence_index_base
sequence_index_color
twobit