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To edit the htseq bash script:
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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.
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runAsPipeline "htseq.sh -p bwaOut -r dm3" "sbatch -p short --mem 4G -t 101:0:0 -n 1" useTmp |
To run the pipeline:
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runAsPipeline "htseq.sh -p bwaOut -r dm3" "sbatch -p short --mem 4G -t 101:0:0 -n 1" useTmp run |
To understand how 'runAsPipeline' works, please visit: Run Bash Script As Slurm Pipeline through rcbio/1.2