Ray can be utilized to classify k-mers in a taxonomy. To do so,
Ray needs a taxonomy.

See these documents for general documentation about graph coloring and taxonomic profiling 
features (called Ray Communities):

	- Documentation/Taxonomy.txt
	- Documentation/BiologicalAbundances.txt


To download the NCBI taxonomy and generate required files:

add this to your PATH:

	export PATH=/home/boiseb01/git-clones/ray/scripts/NCBI-Taxonomy/:$PATH


Then, run this:

	CreateRayInputStructures.sh 


This will generate a directory with these files:

	- NCBI-taxonomy/NCBI-Finished-Bacterial-Genomes
	- NCBI-taxonomy/Genome-to-Taxon.tsv
	- NCBI-taxonomy/TreeOfLife-Edges.tsv
	- NCBI-taxonomy/Taxon-Names.tsv



Now, you can run Ray as usual, but with additional options
to run Ray Communities plugins as well:


mpiexec -n 96 \
Ray \
-k 31 -o Ray-Communities \
-p SeqA_1.fastq SeqA_2.fastq \
-p SeqB_1.fastq SeqB_2.fastq \
-search NCBI-taxonomy/NCBI-Finished-Bacterial-Genomes \
-with-taxonomy NCBI-taxonomy/Genome-to-Taxon.tsv \
NCBI-taxonomy/TreeOfLife-Edges.tsv NCBI-taxonomy/Taxon-Names.tsv 


As usual, you can also put all the arguments in a configuration file like this:

mpiexec -n 96 Ray Ray.conf

where Ray.conf contains

-k 31 -o Ray-Communities 
-p SeqA_1.fastq SeqA_2.fastq 
-p SeqB_1.fastq SeqB_2.fastq 
-search NCBI-taxonomy/NCBI-Finished-Bacterial-Genomes 
-with-taxonomy NCBI-taxonomy/Genome-to-Taxon.tsv 
NCBI-taxonomy/TreeOfLife-Edges.tsv NCBI-taxonomy/Taxon-Names.tsv 


