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To edit the Bowtie2 and RSEM bash script:
| Code Block |
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nano rsemBowtie2.sh |
To test the pipeline run the following command. Jobs will not be submitted to the scheduler.
| Code Block |
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runAsPipeline "rsemBowtie2.sh -r mm10" "sbatch -p short --mem 6G -t 2:0:0 -n 1" useTmp # this is a test run |
To run the pipeline:
| Code Block |
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runAsPipeline "rsemBowtie2.sh -r dm3mm10" "sbatch -p short --mem 6G -t 2:0:0 -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/1.21