run_snpsea.job

#!/bin/bash
# Run SNPSEA on the Sun Grid Engine (SGE) cluster at Broad Institute.
#
# Launch the job:
#     qsub run_snpsea.job
#
# Monitor the progress:
#     qstat

# Name the job
#$ -N snpsea

# Combine stdout and stderr
#$ -j y
#$ -o gridengine_output.out

# Use some memory
#$ -l h_vmem=8G

# Parallel with 6 cores
#$ -pe smp 6

# Run in current working directory
#$ -cwd

# Run time in hours minutes seconds
#$-l h_rt=00:30:00
#$-l s_rt=00:30:00

source /broad/software/scripts/useuse
reuse GSL
reuse GCC-5.2

# snpsea directory
dir=/home/unix/slowikow/work/snpsea

# Some expression files
FANTOM5=${dir}/data/FANTOM2014/FANTOM5.gct.gz
GeneAtlas=${dir}/data/GeneAtlas2004/GeneAtlas2004.gct.gz

snplist=${dir}/data/manuscript/Celiac_disease-Trynka2011-35_SNPs.gwas

expression=${GeneAtlas}

out=$(pwd)/output/$(basename ${expression})_$(basename ${snplist})
mkdir -p ${out}

${dir}/bin/snpsea \
  --snps ${snplist} \
  --gene-matrix ${expression} \
  --gene-intervals ${dir}/data/NCBI/NCBIgenes2013.bed.gz \
  --out ${out} \
  --score total \
  --snp-intervals ${dir}/data/TGP/TGP2011-r2_0.5-hapmap_3-EUR.bed.gz \
  --null-snps ${dir}/data/Lango2010/Lango2010.txt.gz \
  --slop 1e5 \
  --threads 6 \
  --null-snpsets 0 \
  --min-observations 100 \
  --max-iterations 1e7