To run Ray on all these 765 samples, we used SilverRay.
SilverRay calls Ray Meta and Ray Communities with a 
dynamically generated command.

SilverRay is a very small script that lists the sequence files
from a sample directory, and generates the ray command (mpiexec -n XYZ Ray ...)
to assemble with Ray Meta and to profile with Ray Communities.


To run the scripts in this directory, you need to get NGS-Pipelines
which includes SilverRay.

You will also need to install a driver in Drivers to tell where is your
taxonomy, your reference sequences, and so on.



Example:

source /rap/nne-790-ab/software/NGS-Pipelines/LoadModules.sh

SilverRay 31 SRS065335 64 SRS065335-Ray-2012-09-08.1



	generates this command:


mpiexec -n 64 Ray \
 -o \
 Assembly \
 -k \
 31 \
 -p \
 Sample/SRR062290_1.fastq.gz \
 Sample/SRR062290_2.fastq.gz \
 -p \
 Sample/SRR062293_1.fastq.gz \
 Sample/SRR062293_2.fastq.gz \
 -search \
 /rap/nne-790-ab/genomes/EMBL_CDS+GO/EMBL_CDS_Sequences \
 -gene-ontology \
 /rap/nne-790-ab/genomes/EMBL_CDS+GO/000-Ontologies.txt \
 /rap/nne-790-ab/genomes/EMBL_CDS+GO/000-Annotations.txt \
 -search \
 /rap/nne-790-ab/genomes/RayKmerSearchStuff/last-build/ARDB \
 -search \
 /rap/nne-790-ab/genomes/RayKmerSearchStuff/last-build/Bacteria-Genomes \
 -search \
 /rap/nne-790-ab/genomes/RayKmerSearchStuff/last-build/HumanChromosomes \
 -search \
 /rap/nne-790-ab/genomes/RayKmerSearchStuff/last-build/NCBI-Bacteria_DRAFT \
 -search \
 /rap/nne-790-ab/genomes/RayKmerSearchStuff/last-build/Viruses-Genomes \
 -with-taxonomy \
 /rap/nne-790-ab/genomes/taxonomy/last-build/Genome-to-Taxon.tsv \
 /rap/nne-790-ab/genomes/taxonomy/last-build/TreeOfLife-Edges.tsv \
 /rap/nne-790-ab/genomes/taxonomy/last-build/Taxon-Names.tsv

