Containers and Workflows in Bioinformatics

Singularity tutorial

💬 In this tutorial we get familiar with the basic usage of Singularity containers.

To run these exercises in Puhti, use sinteractive.

sinteractive --account project_xxxx   # Change the xxxx for the project number

Getting started

Download a test container image from allas.

 wget  https://a3s.fi/saren-2001659-pub/tutorial.sif
 ls -lh tutorial.sif

As you can see, the container is a single file. In this case the container is very bare-bones, and thus quite small, about 50 MB.
- Actual application containers are typically larger, since they also contain the software installation, and may in some cases include some reference data etc.

Basic usage

💬 There are three basic ways to run software in a Singularity container:

Singularity exec

To execute a command inside the container, the command is singularity exec.
```
 singularity exec tutorial.sif hello_world
```
Compare the outputs of the following commands:
```
 cat /etc/*release
 singularity exec tutorial.sif cat /etc/*release
```
- The first command is run in the host. The second command is run inside the container.

💭 The tutorial container is based on Ubuntu 18.04. The host and the container use the same kernel, but the rest of the system can vary.

That means a container can be based on a different Linux distribution than the host (as long as they are kernel-compatible), but can’t run a totally different OS like Windows or macOS.

Singularity run

💬 When containers are created, a standard action, called the runscript is defined. Depending on the container, it may simply print out a message, or it may launch a program or service inside the container.

💭 If you are using a container created by somebody else, you will need to check the documentation provided by the creator for details.

In our test container it prints out a simple message:
```
 singularity run tutorial.sif
```
Give the container image execute rights and you can also run it directly:
```
 chmod u+x tutorial.sif
 ./tutorial.sif
```

You can see the actual script with command:

 singularity inspect --runscript tutorial.sif

Singularity shell

Open a shell inside the container.
```
 singularity shell tutorial.sif
```
You can see the command prompt change to Singularity>. You can now run any software inside the container interactively:
```
 hello_world
```
Exit the container with:
```
 exit
```

Getting help

You can check if the creator of the container has included any help on the usage:

singularity run-help tutorial.sif

Adding this help is, however, optional, and in many containers it is missing. In those case yoy could check e.g. the developers web site for details.

For software installed by CSC, check Docs CSC.

More information

💬 This tutorial is meant as a brief introduction to get you started.

☝🏻 When searching the internet for instruction, pay attention that the instructions are for the same version of Singularity that you are using. There has been some command syntax changes etc. between the versions, so older instructions may not work with copy-paste.

💡 For authoritative instructions see Singularity documentation.

This site is open source. Improve this page.