...
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:
| Code Block |
|---|
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.
| Code Block |
|---|
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:
| Code Block |
|---|
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