Singularity to run containers

Set up

• For Mac.
• See: https://sylabs.io/guides/3.5/admin-guide/installation.html#installation-on-windows-or-mac

The main steps are:

$ /usr/bin/ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"

$ 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

• open terminal
• vagrant ssh

Check it

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

Get a container image

• e.g. from DockerHub https://hub.docker.com/
• e.g. https://hub.docker.com/r/pegi3s/seqkit
• the user is pegi3s
• the image is seqkit
• singularity pull docker://pegi3s/seqkit

Get a file

• e.g. FastQ sequences
• wget https://zenodo.org/record/1009308/files/pacbio.fq

Use the container to run a tool

• use the exec command
• singularity exec docker://pegi3s/seqkit seqkit stats pacbio.fq

• this runs seqkit stats on pacbio.fq

• run again and save output to file
• singularity exec docker://pegi3s/seqkit seqkit stats pacbio.fq > pac-stats.txt

Where are the files

• pwd to see where you are, then ls
• Singularity can access these files.
• Note: Singularity containers are read-only. Can’t create or edit files.
• The file pac-stats.txt will be in your current directory (of the virtual machine).