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Container_Tutorial.md

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BME 2024 Using and creating Containers

Tutorial loosely based on https://docs.sylabs.io/guides/2.6/user-guide/quick_start.html

Containers are great to familiarize yourself with as a bioinformatician, as they can solve many issues with reproducibility. This tutorial only goes over the absolute basics so you are familiar with using containers if you haven't before.

Environments - Conda

First let's allocate some resources for our session and load singularity

salloc --partition=instruction -N 1 -n 1 -t 03:00:00 
ssh ${SLURM_NODELIST}

module load singularity-ce/singularity-ce.4.1.4

Pulling and building an existing image with Singularity

singularity pull shub://vsoch/hello-world 

singularity build hello-world.simg shub://vsoch/hello-world

Now we can interact with our container either via an interactive session withsingularity shell

singularity shell hello-world.simg

# try running the following commands 
whoami
id

# to leave your shell you can just use 
exit

We can also run container without first entering into it with shell

singularity run hello-world.simg

You can also use run with containers directly from shub and docker

singularity run shub://GodloveD/lolcow

Here are a few more useful commands you can use to check out your containers

singularity inspect hello-world.simg

If we want to just run a single command within our container we can use singularity exec

singularity exec hello-world.simg ls

tricky things with containers

One of the most common issues when working with containers is not mounting your files correctly. This means that you enter into your container and can't find the datafiles you wanted to work with. Singularity automatically will mount your execution directory, home directory, and /tmp, but you may want to mount other locations like this

# first let's create or select a file that we want to mount
mkdir ~/testData

nano ~/testData/data.txt
# write some text into the file, it doesn't matter what 

# now we can mount that directory when we execute a command in our container 

singularity exec --bind ~/testData:/mnt hello-world.simg cat /mnt/data.txt

That exec command should show you the contents of data.txt

finding containers

There are a number of container repositories that are compatible across different container platforms. Often when you need a container there is an existing one you can use online. Here are some places you can find containers
https://biocontainers.pro/registry https://quay.io/ https://hub.docker.com/

Now go find a container that has some software you are familiar with, pull the image, and see if you can view the software documentation with a singularity exec command

It should look something like this

singularity exec image.simg softwareName --help

Now you should be prepared to find and use containers, however there is a lot more functionality for both singularity (and docker) that we didn't cover here. Here are some additional related tutorials that I recommend if you find yourself needing to use containers:

Docker

Create your own container image with docker