format_STAR_output_pipeline_cluster_slurm_part1.sh

#!/bin/sh

#SBATCH --partition=lowmem

#
# ==============================================================================================
# format_STAR_output_pipeline_cluster_slurm_part1:
#
# Description: The next pipeline run format_STAR_output_per_sample.sh in the cluster per sample,
#		given a path with the STAR files. After this, it will be necessary to run 
#		format_STAR_output_pipeline_cluster_part2.sh
#
# Input: arg[1] --> path to the STAR output file (one folder per sample)
#	 arg[2] --> path to the GTF annotation file
#    arg[3] --> path to the Junckey scripts
# ==============================================================================================

io_dir=$1
gtf_dir=$2
scripts_dir=$3

#source /usr/local/sge/default/common/settings.sh

echo "Starting execution. "$(date)
echo "Sending jobs to gencluster..."

#Store the path where the scripts are
#MYSELF="$(readlink -f "$0")"
#scripts_dir="${MYSELF%/*}"
#scripts_dir="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"


for sample in $(ls -d "$io_dir"/*);do
	echo "Processing sample $sample..."
	#Get only the exons from the gtf and remove the comments
    	#grep -v "##" $(echo $gtf_dir) | awk '{ if ($3 == "exon") print }' > "$gtf_dir".aux
	#command="sbatch -J format_STAR_"$cnt" $(echo $scripts_dir)/format_STAR_output_per_sample_slurm.sh $(echo $sample) $(echo $gtf_dir)"
	#echo $command
	sbatch -J $(echo ${sample##*/})_Junckey $(echo $scripts_dir)/format_STAR_output_per_sample_slurm.sh $(echo $sample) $(echo $gtf_dir) $(echo $scripts_dir)
	#qsub -N format_STAR_"$cnt" -S /bin/sh -cwd -q bigmem,long,normal -pe serial 2 -b y $command
done

echo "When all the jobs have finished, run format_STAR_output_pipeline_cluster_slurm_part2.sh"
echo "End of execution. "$(date)

exit 0