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srun --pty -p interactive -t 0-02:0:0 --mem 2000MB -n 1 /bin/bash |
Make alignment using: STAR through module rcbio/1.1 , bowtie2 through module rcbio/1.1 or bwa through module rcbio/1.1
After alignment finishes, go to that folder, for example star
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module load gcc/6.2.0 python/2.7.12 rcbio/1.13.3 cp /n/app/rcbio/1.13.3/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.
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To understand how 'runAsPipeline' works, how to check output, how to re-run the pipeline, please visit: Run Bash Script As Slurm Pipeline through rcbio/1.1
Now you are ready to run an rcbio workflow
To instead run the workflow on your own data, transfer the sample sheet to your local machine following this wiki page and modify the sample sheet. Then you can transfer it back to O2 under your account, then go to the build folder structure step.