Singularity-recipes

This repository collects recipes for building singularity containers.
Currently singularity definition files and Dockerfiles are available, though Dockerfiles should be the preferred way for building the containers.
The python script dockerfile2sif.py helps to locally build a .sif singularity image from a Dockerfile (i.e. without using dockerhub).

Building a singularity container from a singularity definition file

sudo singularity build image.sif definitionfile.def

Building a singularity container from a Dockerfile

The dockerfile2sif.py script allows to create a .sif singularity container from a Dockerfile.
(A docker installation is needed for this.) Run the script via:

python dockerfile2sif.py /path-to-Dockerfile image-name

The singularity image will be created using a temporary .tar version of the docker image that will automatically be deleted. For creating the image, 'sudo' privileges are needed.

Run singularity containers

For an interactive shell session:
singularity shell image.sif

To run a specific command:
singularity exec image.sif command

Run jupyter notebooks inside a container

To run a jupyter notebook you need to pass the --bind option to tell singularity where to write temporary session data.
So for example you can run a notebook directly using:
singularity exec --bind /tmp:/run/user python2.sif jupyter notebook

Or using the interactive shell:

1. singularity shell --bind /tmp:/run/user python2.sif
2. jupyter notebook

Tips when running docker & singularity on a system with little memory

Change singularity cache and tmp directories: SINGULARITY_TMPDIR and
SINGULARITY_CACHEDIR

Clean singularity cache: sudo singularity cache clean

Clean Docker: sudo docker system prune or sudo docker image prune and sudo docker contaienr prune