ROP analysis of multiple sample via qsub

In case you have many files you can submit multiple jobs using qsub.

Run ROP for all the samples at once :

• Run a single sample from the command line to make sure there are no unexpected errors.

• Create a text file with all of the file names (no extensions) that will be run

ls *fasta | awk -F ".fasta" '{print $1}'>sample.txt 

• Create a run.sh file for each sample that will be run.

#general example
while read line; do echo "<your command here>" > run_${line}.sh; done < <path to file with all sample names>

#implementation for ROP tool
while read line; do echo "python /u/home/s/serghei/code2/rop/rop.py --qsubArray --skipQC /u/home/b/brigitta/scratch/gtex/data/${line}.fasta $PWD/${line}" > run_${line}.sh; done<../sample.txt

Please follow the following steps:

ls run*sh | awk '{i+=1;print "qsub -cwd -V -N rop"i" -l h_data=16G,time=24:00:00 "$1}' > all.sh

Now you have all.sh with individual qsub command per sample. To run all the qsubs from all.sh do the following:

• chmod u+x all.sh
• nohup ./all.sh &