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Singularity
Containerization software used to run SMRT Link in an isolated, portable environment.
Singularity is only supported on Linux. To get it on your Windows machine, first install Windows Subsystem for Linux.
At the time of writing this, Singularity is not available Ubuntu's package manager. Instead:
- download the package from Github
- install dependencies
- use
sudo dpkg -i <path-to-package>to install singularity.
The target machine for deploying the container is administered by BYU ORC, and BYU ORC only supports Singularity on their systems.
We used Singularity CE 4.1 from Sylabs. Maybe someday Apptainer will be a more attractive version.
Most features work out of the box in WSL, however anything requiring systemd will not work because WSL Ubuntu doesn't use systemd.
This includes starting instances as root because, if you are root, Singularity will try to use systemd to manage resources available to the instance.
You can prevent this by modifying singularity's config file (usually /etc/singularity/singularity.conf) so that "systemd cgroups = no".