Start an interactive job, with a walltime of 2 hours, 2000MB of memory.
srun --pty -p interactive -t 0-02:0:0 --mem 2000MB -n 1 /bin/bash
Make alignment using: STAR through module rcbio/1.1 , bowtie2 through module rcbio/1.1 or bwa through module rcbio/1.1
After alignment finishes, go to that folder, for example star
cd /n/scratch3/users/a/abc123/star
Copy the example htseq bash script:
module load gcc/6.2.0 python/2.7.12 rcbio/1.1 cp /n/app/rcbio/1.1/bin/htseq.sh .
Now you can modify the options as needed. For example, if your file are huge, you may need increase mem and runtime -t for sbatch command.
To edit the htseq bash script:
nano htseq.sh #or if you have single end reads nano htseqSingle.sh
To test the pipeline run the following command if you did alignment by bwa as on this page. If you did alignment using bowtie2 following this page, please change -p bwaOut to -p bowtieOut, or if you used star following this page, please change -p bwaOut to -p starOut. Jobs will not be submitted to the scheduler.
runAsPipeline "htseq.sh -p bwaOut -r dm3" "sbatch -p short --mem 4G -t 1:0:0 -n 1" useTmp #or if you have single end reads runAsPipeline "htseqSingle.sh -p bwaOut -r dm3" "sbatch -p short --mem 4G -t 1:0:0 -n 1" useTmp # this is a test run
To run the pipeline:
runAsPipeline "htseq.sh -p bwaOut -r dm3" "sbatch -p short --mem 4G -t 1:0:0 -n 1" useTmp run 2>&1 | tee output.log #or if you have single end reads runAsPipeline "htseqSingle.sh -p bwaOut -r dm3" "sbatch -p short --mem 4G -t 1:0:0 -n 1" useTmp run 2>&1 | tee output.log # notice here 'run 2>&1 | tee output.log' is added to the command
To understand how 'runAsPipeline' works, please visit: Run Bash Script As Slurm Pipeline through rcbio/1.1