generate_singularity: Generate Singularity Definition File

In Capsule: Comprehensive Reproducibility Framework for R and Bioinformatics Analysis

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"
)

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

Value

List of generated file paths

Examples

## Not run: 
generate_singularity(
  output_dir = tempdir(),
  project_name = "my_analysis",
  system_deps = c("samtools", "bwa")
)

## End(Not run)

Capsule documentation built on Nov. 11, 2025, 5:14 p.m.