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To edit the htseq bash script:

nano htseq.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


# 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

# 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/1.2