gistfile1.sh

#!/bin/bash
#PBS -N RayRay-ERS006494-__SAMPLE__-2013-05-24-2
#PBS -o RayRay-ERS006494-__SAMPLE__-2013-05-24-2.o
#PBS -e RayRay-ERS006494-__SAMPLE__-2013-05-24-2.e
#PBS -A nne-790-ac
#PBS -l walltime=48:00:00
#PBS -l nodes=8:ppn=8
#PBS -q default

cd $PBS_O_WORKDIR

module load compilers/gcc/4.7.2
module load mpi/openmpi/1.6.3_gcc

RayRayMothership="mpiexec"
Ray="apps/__SAMPLE__"

$RayRayMothership -n 64 $Ray \
-write-kmers \
 -o \
 RayRay-ERS006494-__SAMPLE__-2013-05-24-2 \
 -k \
 31 \
 -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 \
-p ERS006494/ERR011117_1.fastq.gz ERS006494/ERR011117_2.fastq.gz \
-p ERS006494/ERR011118_1.fastq.gz ERS006494/ERR011118_2.fastq.gz \
-p ERS006494/ERR011119_1.fastq.gz ERS006494/ERR011119_2.fastq.gz \
-p ERS006494/ERR011120_1.fastq.gz ERS006494/ERR011120_2.fastq.gz \
-p ERS006494/ERR011121_1.fastq.gz ERS006494/ERR011121_2.fastq.gz \
-p ERS006494/ERR011122_1.fastq.gz ERS006494/ERR011122_2.fastq.gz \
-p ERS006494/ERR011123_1.fastq.gz ERS006494/ERR011123_2.fastq.gz \
 . .,  ..n.