DiamondRay

#!/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

##
## base command
##

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

##
## add sequence reads
##

command="$command $pairs"

##
##  ontology profiling
##

# 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 "

##
## taxonomy profiling
##

command="$command \
 -search \
 $GENOMES_DIRECTORY/RayKmerSearchStuff/last-build/ARDB \
 -search \
 $GENOMES_DIRECTORY/RayKmerSearchStuff/last-build/Bacteria-Genomes \
 -search \
 $GENOMES_DIRECTORY/RayKmerSearchStuff/last-build/Bacteria-ProteinCodingGenes \
 -search \
 $GENOMES_DIRECTORY/RayKmerSearchStuff/last-build/Bacteria-RNAGenes \
 -search \
 $GENOMES_DIRECTORY/RayKmerSearchStuff/last-build/HumanChromosomes \
 -search \
 $GENOMES_DIRECTORY/RayKmerSearchStuff/last-build/NCBI-Bacteria_DRAFT \
 -search \
 $GENOMES_DIRECTORY/RayKmerSearchStuff/last-build/Viruses-Genomes \
 -with-taxonomy \
 $GENOMES_DIRECTORY/taxonomy/last-build/Genome-to-Taxon.tsv \
 $GENOMES_DIRECTORY/taxonomy/last-build/TreeOfLife-Edges.tsv \
 $GENOMES_DIRECTORY/taxonomy/last-build/Taxon-Names.tsv"

#echo $command

DarkFishTechnology_runCommand 0 "$command"