Anna Syme

Click name ↑ to return to homepage

Singularity to run containers

Set up

The main steps are:

$ /usr/bin/ruby -e "$(curl -fsSL"

$ brew cask install virtualbox && \
    brew cask install vagrant && \
    brew cask install vagrant-manager

$ mkdir vm-singularity && \
    cd vm-singularity

$ export VM=sylabs/singularity-3.5-ubuntu-bionic64 && \
    vagrant init $VM && \
    vagrant up && \
    vagrant ssh

If already set up

Check it

singularity version
singularity --help
singularity help pull \\or other subcommand

Get a container image

Get a file

Use the container to run a tool


Where are the files