R-bioconductor

Introduction

R is a system for statistical computation and graphics. This is a r/4.4.2 Apptainer image with main R packages and Bioconductor installed. RStudio is an integrated development environment (IDE) for the R statistical computation and graphics system.

For more information, please check:

Home page: https://www.rstudio.com/products/rstudio/

Home page: https://www.r-project.org/

Note

Please follow the recommended citation guidelines from the developers when you use the tool in research.

Versions

Cluster	Version(s)
ANVIL	3.20-R-4.4.3, 3.22-r-4.5.1, 3.23-r-4.6.0
BELL	3.20-R-4.4.3, 3.22-r-4.5.1, 3.7-R-3.5.1, 3.23-r-4.6.0
GAUTSCHI	3.20-R-4.4.3, 3.22-r-4.5.1, 3.23-r-4.6.0
NEGISHI	3.20-R-4.4.3, 3.22-r-4.5.1, 3.7-R-3.5.1, 3.23-r-4.6.0
SCHOLAR	3.20-R-4.4.3, 3.23-r-4.6.0

Commands

• R

• Rscript

Module

You can load the modules by:

module load biocontainers
module load r-bioconductor

Example job

Warning

Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run r-bioconductor on our clusters:

Anvil

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -p wholenode        # Partition name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=r-bioconductor
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers r-bioconductor

# Your r-bioconductor workflow...

Bell, Gautschi, or Negishi

#!/bin/bash
#SBATCH -A mygroup     # Group name
#SBATCH -p cpu         # Partition name
#SBATCH -q normal      # QOS name (optional)
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=r-bioconductor
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers r-bioconductor

# Your r-bioconductor workflow...

Gautschi-AI

#!/bin/bash
#SBATCH -A mygroup     # Group name
#SBATCH -p ai          # Partition name
#SBATCH --gres=gpu:1   # Number of GPUs
#SBATCH -q normal      # QOS name (optional)
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=r-bioconductor
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers r-bioconductor

# Your r-bioconductor workflow...

Gilbreth

#!/bin/bash
#SBATCH -A mygroup     # Group name
#SBATCH -p a100        # Partition name
#SBATCH --gres=gpu:1   # Number of GPUs
#SBATCH --mem=2G       # Memory
#SBATCH -q normal      # QOS name (optional)
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=r-bioconductor
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers r-bioconductor

# Your r-bioconductor workflow...

Scholar

#!/bin/bash
#SBATCH -A queue     # Queue name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=r-bioconductor
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers r-bioconductor

# Your r-bioconductor workflow...