Apptainer (Singularity) ​

Apptainer, previously known as Singularity, provides application containers for Linux that is also compatible with Docker.

Install with Conda ​

Requirements

  • 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 Apptainer. If you have not set channels yet make sure to add it:

bash
conda config --add channels conda-forge

Install Apptainer (Singularity) in conda environment

Create environment and install Apptainer (Singularity):

bash
conda create -n apptainer -c conda-forge "apptainer"

Activate your apptainer environment and try running Apptainer:

bash
conda activate apptainer

apptainer --help

Common practices and commands ​

All information is collected from the official Apptainer documentation.

Pull Docker image ​

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

bash
#-- Example 
apptainer pull docker://godlovedc/lolcow
bash
#-- Example
apptainer build  -B $TMPDIR lolcow.sif docker://godlovedc/lolcow

Run Docker image ​

For demonstration, let’s use an easy (though somewhat useless) example of lolcow.sif image from Docker:

bash
apptainer pull docker://godlovedc/lolcow
#-- The above command will save the alpine image from the Container Library as lolcow.sif

To start an instance, you should follow below pattern:

apptainer instance start -B $TMPDIR      <image>    <instance-name>
bash
apptainer instance start -B $TMPDIR lolcow.sif instance1

This command causes Apptainer 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:

bash
apptainer instance list

INSTANCE NAME    PID        IP    IMAGE
instance1        3661427          /mnt/scratch/tmp/rootfs-728963423/root

Stop running container ​

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

bash
apptainer instance stop instance1

Where are the images stored ? ​

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

bash
$APPTAINER_CACHEDIR/cache/library
$APPTAINER_CACHEDIR/cache/oci
$APPTAINER_CACHEDIR/cache/oci-tmp

Temporary file storage ​

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

bash
#-- Example
apptainer shell -B $TMPDIR docker://ubuntu