RCC has the gemBS-rs DNA Methylation Sequencing Analysis pipeline available on our HPC systems. The version we have available uses the Singularity container system. This does not require any special considerations on the part of the user however containers are helpful as they are useful for promoting reproducible research.
Using gemBS-rs on HPC Systems
In order to use gemBS-rs, all you need to do is load the gemBS module and then call the program. This can be done either interactively or non-interactively.
Interactive use of gemBS-rs
Shown below are the commands needed to run gemBS. Simply replace [options] and [arguments] with the gemBS-specific arguments or input files and options needed for your particular job. More details are available at the gemBS-rs Documentation Site.
module load gembs gemBS [options] [arguments]
Non-Interactive Use of gemBS-rs
If you want to submit a job using gemBS-rs, simply create a submit script such as the one that follows. Adjust your #SBATCH parameters and gemBS options and arguments as necessary according to your needs and the RCC Job Reference and the gemBS-rs Documentation Site.
#!/bin/bash #SBATCH -J myTestJob #SBATCH -n 4 #SBATCH -p genacc_q #SBATCH -t 10:00:00 #SBATCH --mail-type=ALL module load gembs srun gemBS [options] [arguments]