# Singularity

Singularity (opens new window) provides application containers for Linux that is also compatible with Docker.

# Install with Conda


  • Conda (miniconda), see our Conda tutorial for more details.
  • Conda channels: conda-forge, bioconda

Add the conda-forge channel

You will need the conda-forge channel to install Singularity. If you have not set channels yet make sure to add it:

conda config --add channels conda-forge

Install singularity in conda environment

Create environment and install Singularity:

conda create -n singularity -c conda-forge "singularity>=3.0.0"

Activate your singularity environment and try running Singularity:

conda activate singularity

singularity --help

# Common practices and commands

All information is collected from official Singularity documentation (link above).

# Pull Docker image

You can use the pull (opens new window) and build (opens new window) commands to download pre-built images from an external resource like the Container Library (opens new window) or Docker Hub (opens new window).

#-- Example
singularity pull library://library/default/alpine
#-- Example
singularity build  -B $TMPDIR lolcow.sif docker://godlovedc/lolcow

# Run Docker image

For demonstration, let’s use an easy (though somewhat useless) example of alpine_latest.sif (opens new window) image from the container library (opens new window):

singularity pull library://alpine
#-- The above command will save the alpine image from the Container Library as alpine_latest.sif.

To start an instance, you should follow below pattern:

singularity instance start -B $TMPDIR      <image>    <instance-name>
singularity instance start -B $TMPDIR alpine_latest.sif instance1

This command causes Singularity to create an isolated environment for the container services to live inside.

# Listing running containers

One can confirm that an instance is running by using the instance list command like so:

singularity instance list

instance1        12715    /home/ysub/alpine_latest.sif

# Stop running container

When you are finished with your instance you can clean it up with the instance stop command as follows:

singularity instance stop instance1

# Where are the images stored ?

By default, Singularity will create a set of folders in your $SINGULARITY_CACHEDIR directory for docker layers, Cloud library images, and metadata, respectively:


# Temporary file storage

By default, Singularity won't recognize lab tmp storage. You can apply lab tmp storage location /mnt/scratch/tmp to a container using -B $TMPDIR variable

#-- Example
singularity shell -B $TMPDIR docker://ubuntu
Last Updated: 9/27/2023