Start an interactive job, with a walltime of 2 hours, 2000MB of memory.
srun --pty -p interactive -t 0-02:0:0 --mem 2000MB -n 1 /bin/bash
Create a working directory on scratch and change into the newly-created directory. For example, for user abc123, the working directory will be
mkdir /n/scratch3/users/a/abc123/rsem cd /n/scratch3/users/a/abc123/rsem
Load modules and setup path, then copy some test data. For details to use your own data, please visit this page: Build Folder Structures From Sample Sheet for rcbio NGS Workflows
module load gcc/6.2.0 python/2.7.12 rcbio/1.1 cp /n/shared_db/misc/rcbio/data/fruitFlyFastq/sampleSheet.xlsx . buildSampleFoldersFromSampleSheet.py sampleSheet.xlsx
Copy the example rsemBowtie2 bash script:
cp /n/app/rcbio/1.1/bin/rsemBowtie2.sh .
Now you can modify the options as needed. Please reference the http://deweylab.github.io/RSEM/ if you have any questions.
To edit the Bowtie2 and RSEM bash script:
nano rsemBowtie2.sh
To test the pipeline run the following command. Jobs will not be submitted to the scheduler.
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:
runAsPipeline "rsemBowtie2.sh -r mm10" "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/1.1