Andrea Telatin
Andrea Telatin Senior bioinformatician at the Quadram Institute Bioscience, Norwich.

Singularity for bioinformatics

Singularity for bioinformatics

A basic introduction to Singularity containers

What is a container?

In simple words, a container is an isolated system that shares with the host only the kernel, allowing the installation of a custom set of libraries, dependencies and tools that will not conflict with the existing installation in the host.

It’s a more isolated system if compared with a “conda environment”, but not as independent as a complete virtualization (e.g. VirtualBox): the former shares several libraries and building tools with the host system, the latter will create a virtual computer (a dedicated processor, that can even be different to the real one, a dedicated RAM, that is necessarily a fraction of the total installed RAM…).

As a rule of the thumb, virtualization is necessary only when the current architecture (e.g. CPU) or system (e.g. Windows is required but Linux is installed) cannot support a specific software. In all the other cases, a container is the ideal solution that will guarantee to work in a more robust fashion when compared with conda environments, and in a more portable way.

What is Singularity?

The most popular containerization ecosystem is Docker. Singularity became the Docker alternative for academics working with HPCs. Singularity allows to execute software available in a container with some interesting features:

  • The container runs in the user space: no root access is required
  • The container can “see” the filesystem of the host as any other tool
  • A container is a single file: it’s easy to share them and use the same container in multiple servers

How does it work?

Suppose you have a Singularity image containing the assembly software “SPAdes”, this means you can simply run SPAdes from the container.

In a native installation you can run SPAdes as:

1 -1 path/to/read_R1.fq -2 path/to/read_R2.fq -o contigs/

A singularity container is stored in an image that is a single file. There are several possibilities when it come to its extension: from no extension at all, to .sif, .simg (singularity image). Let’s assume our image is called spades-3.14.simg, we can execute it as:

singularity run path/to/spades-3.14.simg  -1 path/to/read_R1.fq -2 path/to/read_R2.fq -o contigs/

As simple as this!

More about running software from an image

A singularity image is a complete Linux system, so it carries a lot of software in it. When building an image the user can define an “entry point”, that is a default binary to be executed. In the SPAdes example we defined to be such default binary, hence we didn’t need to specify its name in our previous example.

If we want to execute a specific binary (suppose spades-bwa, also shipped with SPAdes), the syntax is singularity exec BINARY:

singularity exec path/to/spades-3.14.simg spades-bwa --help

When debugging an image we might want to see the world from its inside, that is having a shell from its system. This can be simply done with:

singularity shell path/to/spades-3.14.simg

This will open a shell inside the container, and when we are done we can simply type exit to return to our host shell. Remember that inside that shell you’ll have only the tool installed with it (for example: nano) and the image itself will be (should be) write only.

Some notes on Singularity for bioinformatics

I’ll post some basic guide on how to install singularity and how to build a custom image soon.

Meanwhile some notes are available in a dedicated repository.