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Using Singularity Images on the HPC

This guide explains how to use the Singularity images deployed via the GitHub Actions workflow.

Available Images

The workflow deploys the following Singularity images to the HPC cluster:

/data/barskilab/scidap_server/singularity_images/biowardrobe2_scidap-deseq:v0.0.30.sif

The version may change as new versions are deployed. You can check the current version in:

/data/barskilab/scidap_server/singularity_images/scidap-deseq-version.txt

Running the Singularity Container

Interactive Mode

To start an interactive shell session with the container:

# Load Singularity module
module load singularity/3.7.0

# Start interactive shell
singularity shell /data/barskilab/scidap_server/singularity_images/biowardrobe2_scidap-deseq:v0.0.30.sif

Running Commands

To run a specific command within the container:

# Load Singularity module
module load singularity/3.7.0

# Run R script
singularity exec /data/barskilab/scidap_server/singularity_images/biowardrobe2_scidap-deseq:v0.0.30.sif Rscript your_analysis.R

Binding Directories

To access directories from the host system within the container:

# Load Singularity module
module load singularity/3.7.0

# Run with bound directories
singularity exec --bind /path/to/data:/data,/path/to/output:/output \
  /data/barskilab/scidap_server/singularity_images/biowardrobe2_scidap-deseq:v0.0.30.sif \
  Rscript /data/analysis.R

Example Batch Script

Here's an example SLURM batch script to use the container:

#!/bin/bash
#SBATCH --job-name=deseq_analysis
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=4
#SBATCH --mem=16G
#SBATCH --time=2:00:00
#SBATCH --output=deseq_%j.out

# Load Singularity module
module load singularity/3.7.0

# Define input/output paths
INPUT_DIR=/path/to/input
OUTPUT_DIR=/path/to/output
SCRIPT_PATH=/path/to/script.R

# Run analysis in container
singularity exec \
  --bind ${INPUT_DIR}:/input,${OUTPUT_DIR}:/output \
  /data/barskilab/scidap_server/singularity_images/biowardrobe2_scidap-deseq:v0.0.30.sif \
  Rscript ${SCRIPT_PATH}

Troubleshooting

Common Issues

  1. Module not found:

    singularity: command not found

    Solution: Ensure you've loaded the Singularity module with module load singularity/3.7.0

  2. Permission denied:

    FATAL: container creation failed: mount /proc/self/fd/3->/var/singularity/mnt/session/rootfs error: permission denied

    Solution: Check file permissions or use a compute node where you have appropriate permissions

  3. Binding errors:

    ERROR: Failed to attach /path/to/data to /data: no such file or directory

    Solution: Ensure the bind paths exist on both the host and in the container

Getting Help

For additional help:

  1. Check the image documentation in the repository
  2. Contact the HPC support team
  3. File an issue in the GitHub repository