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gemBS-rs is a rewrite of the gemBS pipeline using Rust. gemBS itself is a powerful high-throughput pipeline for DNA methylation sequencing analysis.

gemBS-rs requires an environment module

In order to use gemBS-rs, you must first load the appropriate environment module:

module load gembs

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.

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, gemBS options and arguments as needed, using the RCC Job Reference and gemBS-rs official page for reference.

#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]