...
| Code Block |
|---|
module load gcc/6.2.0 python/2.7.12 rcbio/1.1
cp /n/app/rcbio/1.1/bin/htseq.sh .
##############
note: rcbio/1.1 is not available yet. If you would like to try the version still in development stage, you can run:
export PATH=/home/ld32/rcbioDev/bin:$PATH
cp /home/ld32/rcbioDev/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:
| Code Block |
|---|
nano htseq.sh |
To test the pipeline run the following command if you did alignment by bwa as on this page. Jobs will not be submitted to the scheduler.
| Code Block |
|---|
runAsPipeline "htseq.sh -p starOutbwaOut -ir dm3" "sbatch -p short -t 10:0 -n 1" useTmp |
To run the pipeline:
| Code Block |
|---|
runAsPipeline "htseq.sh -p starOutbwaOut -ir dm3" "sbatch -p short -t 10:0 -n 1" useTmp run |
To understand how 'runAsPipeline' works, please visit: Run Bash Script As Slurm Pipeline