Running Singularity containers from online repositories
Let us try to run a small and simple container from Docker Hub repository. Singularity, will pull the docker image in the cache, convert it and run it. The output should look something like this:
Important - reminder
Environmental variables that will help you to redirect potentially large folders to alternative location - keep in mind that your $HOME folder is relatively small in size.
export PROJECT=project_folder
export SINGULARITY_CACHEDIR=/proj/${PROJECT}/nobackup/SINGULARITY_CACHEDIR
export SINGULARITY_TMPDIR=/proj/${PROJECT}/nobackup/SINGULARITY_TMPDIR
export APPTAINER_CACHEDIR=/proj/${PROJECT}/nobackup/SINGULARITY_CACHEDIR
export APPTAINER_TMPDIR=/proj/${PROJECT}/nobackup/SINGULARITY_TMPDIR
mkdir -p $APPTAINER_CACHEDIR $APPTAINER_TMPDIR
$ singularity run docker://sylabsio/lolcow
INFO: Converting OCI blobs to SIF format
INFO: Starting build...
INFO: Fetching OCI image...
27.2MiB / 27.2MiB [====================================================================================================] 100 % 8.5 MiB/s 0s
45.8MiB / 45.8MiB [====================================================================================================] 100 % 8.5 MiB/s 0s
INFO: Extracting OCI image...
INFO: Inserting Singularity configuration...
INFO: Creating SIF file...
________________________________
< Thu Oct 2 09:35:31 Europe 2025 >
--------------------------------
\ ^__^
\ (oo)\_______
(__)\ )\/\
||----w |
|| ||
fortune | cowsay | lolcat.
date- print current date and time.cowsay- configurable speaking/thinking cow (and a bit more)lolcat- rainbow coloring effect for text console display
Let's run it again.
$ singularity run docker://sylabsio/lolcow
INFO: Using cached SIF image
________________________________
< Thu Oct 2 09:37:31 Europe 2025 >
--------------------------------
\ ^__^
\ (oo)\_______
(__)\ )\/\
||----w |
|| ||
$ singularity cache list
There are 1 container file(s) using 87.96 MiB and 8 oci blob file(s) using 99.09 MiB of space
Total space used: 187.04 MiB
Info
Over time the cache will grow and might easily accumulate unnecessary "blobs". To clean the cache you can run.
$ singularity cache clean
singularity cache clean --dry-run
User requested a dry run. Not actually deleting any data!
INFO: Removing blob cache entry: blobs
INFO: Removing blob cache entry: index.json
INFO: Removing blob cache entry: oci-layout
INFO: No cached files to remove at /home/ubuntu/.singularity/ cache/library
INFO: Removing oci-tmp cache entry: a692b57abc43035b197b10390ea2c12855d21649f2ea2cc28094d18b93360eeb
INFO: No cached files to remove at /home/ubuntu/.singularity/ cache/shub
INFO: No cached files to remove at /home/ubuntu/.singularity/ cache/oras
INFO: No cached files to remove at /home/ubuntu/.singularity/ cache/net
More examples
$ singularity run docker://dctrud/wttr
Info
Excellent course material by the CodeRefinery project
Containers on HPC with Apptainer
metaWRAP - a flexible pipeline for genome-resolved metagenomic data analysis
Here is an example how to use the metaWRAP pipeline from the docker container - installation instructions.
# Original instructions (do NOT run)
$ docker pull quay.io/biocontainers/metawrap:1.2--1
$ singularity pull docker://quay.io/biocontainers/metawrap:1.2--1
INFO: Converting OCI blobs to SIF format
INFO: Starting build...
Getting image source signatures
...
Then, one can start the container and use it interactively.
In this particular case, executing the Singularity container gives us a shell running in the container.
$ ./metawrap_1.2--1.sif
WARNING: Skipping mount /usr/local/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container
Singularity> metawrap --version
metaWRAP v=1.2
To run the tool from the command line (outside of the container, as you would use it in scripts) we need to add the call for the tool.
Original commad in the cript:
$ metawrap binning -o Lanna-straw_initial_binning_concoct -t 20 -a /proj/test/megahit_ass_Lanna-straw/final.contigs.fa --concoct --run-checkm /proj/test/Lanna-straw_reads_trimmed/*.fastq
The command now calls the tool from the Singularity container:
$ singularity exec metawrap_1.2--1.sif metawrap binning -o Lanna-straw_initial_binning_concoct -t 20 -a /proj/test/megahit_ass_Lanna-straw/final.contigs.fa --concoct --run-checkm /proj/test/Lanna-straw_reads_trimmed/*.fastq
Pulling Singularity container from online or local library/repository
- library:// to build from the Container Library
library://sylabs-jms/testing/lolcow - docker:// to build from Docker Hub
docker://godlovedc/lolcow - shub:// to build from Singularity Hub
- path to a existing container on your local machine
- path to a directory to build from a sandbox
- path to a Singularity definition file
Tensorflow
Let's have some tensorflow running. First pull the image from docker hub (~2.6GB).
$ singularity pull docker://tensorflow/tensorflow:latest-gpu
INFO: Converting OCI blobs to SIF format
INFO: Starting build...
Getting image source signatures
...
If you have a GPU card, here is how easy you can get tensorflow running. Note the --nv option on the command line.
$ singularity exec --nv tensorflow_latest-gpu.sif python3
Python 3.8.10 (default, Nov 26 2021, 20:14:08)
[GCC 9.3.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import tensorflow as tf
>>> tf.config.list_physical_devices('GPU')
[PhysicalDevice(name='/physical_device:GPU:0', device_type='GPU')]