ROP analysis of multiple sample

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

• For each run.sh file created, generate a command to run each file and store it on a separate line in a file called myFunc.sh

ls *sh | awk '{i+=1;print "if [ $1 == "i" ];then ./"$1" ;fi"}' > myFunc.sh

• Copy the file myFuncFastWrapper.sh from the ROP tool (/rop/source) to the current directory

cp /u/home/s/serghei/code2/rop/myFuncFastWrapper.sh ./

• Change file permissions as necessary

#change file permissions for myFunc.sh
chmod 755 myFunc.sh

#change file permissions for all .sh files in current directory
chmod 755 *sh

• Find the total number of samples that will be run (number of lines in your myFunc.sh file)

wc -l myFunc.sh

• Lastly, use qsub to submit all of the samples

#general example
qsub -cwd -V -N <your job name> -l h_data=<memory needed per job>,express,time=<time needed per job> -t 1-<number of samples>:1 myFuncFastWrapper.sh

#implementation 
qsub -cwd -V -N rop -l h_data=12G,express,time=04:00:00 -t 1-176:1 myFuncFastWrapper.sh