gistfile1.txt

#!/bin/bash

bf_bin="/stornext/snfs1/next-gen/drio-scratch/bfast_related/versions/production/bfast/bfast"
fq="/stornext/snfs4/next-gen/solid/analysis/solid0099/0099_20100104_2_SL_AWG_HCC_L09_0150_T_000pA_01003244695_1/reads/0099_20100104_2_SL_AWG_HCC_L09_0150_T_000pA_01003244695_1.21.fastq"


for i in `seq 1 72`
do
  cat <<-EOF
  bsub -q normal \
  -J normal$i \
  "${bf_bin} match -A 1 -t -n 8 \
  -f /stornext/snfs4/next-gen/solid/bf.references/h/hsap.36.1.hg18/hsap_36.1_hg18.fa \
  -T /space1/tmp/ \
  -r $fq \
  > /dev/null"
EOF
done

for i in `seq 1 144`
do
  cat <<-EOF
  bsub -q hptest \
  -J hptest$i \
  ${bf_bin} match -A 1 -t -n 8 \
  -f /stornext/snfs4/next-gen/solid/bf.references/h/hsap.36.1.hg18/hsap_36.1_hg18.fa \
  -T /space1/tmp/ \
  -r $fq \
  > /dev/null
EOF
done