#!/bin/bash -l

#Give the name to the job
#$ -N oases_step_by_step

#Send an email when the job is finished (or aborted)
#$ -m ae

#Join the error and output file
#$ -j y

#Sepcify the version of velvet
module load velvet/1.2.10
module load oases/0.2.09

#Run the program
velveth out 21,25,2 -short -fasta test_reads.fa
for k in `seq 21 2 23`
do
    velvetg out_$k -read_trkg yes
done

for k in seq '21 2 23'
do
    oases out_$k
done

velveth merged 23 -long out*/transcripts.fa
velvetg merged -read_trkg yes -conserveLong yes
oases merged -merge yes

echo "done! check merged/ directory for results"