GoldRay

#!/bin/bash

kmerLength=$1
sampleDirectory=$2
processors=$3
outputDirectory=$4

mkdir $outputDirectory
cd $outputDirectory
source $DARK_FISH_TECHNOLOGY

DarkFishTechnology_initializeDirectory
DarkFishTechnology_prepareSample $sampleDirectory
pairs=$(DarkFishTechnology_getPairs)

mpiexec -version &> meta/mpiexec.version
Ray -version &> meta/ray.version

command="mpiexec -output-filename ComputeCore -n $processors Ray -o Assembly -k $kmerLength $pairs"

# EMBL_CDS sequences
geneSequences=$GENOMES_DIRECTORY/EMBL_CDS+GO/EMBL_CDS_Sequences

# annotation for EMBL_CDS objects
annotations=$GENOMES_DIRECTORY/EMBL_CDS+GO/000-Annotations.txt

# ontologies in obo format, as downloaded from geneontologies.org
ontologies=$GENOMES_DIRECTORY/EMBL_CDS+GO/000-Ontologies.txt

command="$command -search $geneSequences -gene-ontology $ontologies $annotations "

DarkFishTechnology_runCommand 0 "$command"