Capsule (version 0.2.0)

generate_singularity: Generate Singularity Definition File

Description

Generate a Singularity/Apptainer definition file for HPC environments. Singularity is commonly used in HPC clusters where Docker is not available.

Usage

generate_singularity(
  output_dir,
  r_version = NULL,
  base_image = "rocker/r-ver",
  conda_env = NULL,
  system_deps = NULL,
  project_name = "reproflow-project"
)

Value

List of generated file paths

Arguments

output_dir

Character. Directory to save Singularity files (required).

r_version

Character. R version to use. Default is current R version.

base_image

Character. Base Docker image. Default "rocker/r-ver"

conda_env

Character. Path to conda environment file. Optional.

system_deps

Character vector. System dependencies to install

project_name

Character. Name for the project

Examples

if (FALSE) {
generate_singularity(
  output_dir = tempdir(),
  project_name = "my_analysis",
  system_deps = c("samtools", "bwa")
)
}