Singularity

Introduction to Singularity

Singularity architecture

_images/singularity_architecture.png

Strengths

Weaknesses

No dependency of a daemon

At the time of writing only good support in Linux

Can be run as a simple user

Mac experimental. Desktop edition. Only running

Avoids permission headaches and hacks

For some features you need root account (or sudo)

Image/container is a file (or directory)

More easily portable

Two types of images: Read-only (production)

Writable (development, via sandbox)

Trivia

Nowadays, there may be some confusion since there are two projects:

They “forked” in 2021. So far they share most of the codebase, but eventually this could be different, and software might have different functionality.

The former is already “End Of Life” and its development continues named as Apptainer, under the support of the Linux Foundation.

Container registries

Container images, normally different versions of them, are stored in container repositories.

These repositories can be browser or discovered within, normally public, container registries.

Docker Hub

It is the first and most popular public container registry (which provides also private repositories).

Example:

https://hub.docker.com/r/biocontainers/fastqc

singularity build fastqc-0.11.9_cv7.sif docker://biocontainers/fastqc:v0.11.9_cv7

Biocontainers

Website gathering Bioinformatics focused container images from different registries.

Originally Docker Hub was used, but now other registries are preferred.

Example: https://biocontainers.pro/tools/fastqc

Via quay.io

https://quay.io/repository/biocontainers/fastqc

singularity build fastqc-0.11.9.sif docker://quay.io/biocontainers/fastqc:0.11.9--0

Via Galaxy project prebuilt images

singularity pull --name fastqc-0.11.9.sif https://depot.galaxyproject.org/singularity/fastqc:0.11.9--0

Galaxy project provides all Bioinformatics software from the BioContainers initiative as Singularity prebuilt images. If download and conversion time of images is an issue, this might be the best option for those working in the biomedical field.

Link: https://depot.galaxyproject.org/singularity/

Running and executing containers

Once we have some image files (or directories) ready, we can run processes.

Singularity shell

The straight-forward exploratory approach is equivalent to docker run -ti biocontainers/fastqc:v0.11.9_cv7 /bin/shell but with a more handy syntax.

singularity shell fastqc-0.11.9.sif

Move around the directories and notice how the isolation approach is different in comparison to Docker. You can access most of the host filesystem.

Singularity exec

That is the most common way to execute Singularity (equivalent to docker exec). That would be the normal approach in a HPC environment.

singularity exec fastqc-0.11.9.sif fastqc

Test a processing of a file from testdata directory:

singularity exec fastqc-0.11.9_cv7.sif fastqc B7_input_s_chr19.fastq.gz

Singularity run

This executes runscript from recipe definition (equivalent to docker run). Not so common for HPC uses. More common for instances (servers).

singularity run fastqc-0.11.9.sif

Environment control

By default Singularity inherits a profile environment (e.g., PATH environment variable). This may be convenient in some circumstances, but it can also lead to unexpected problems when your own environment clashes with the default one from the image.

singularity shell -e fastqc-0.11.9.sif
singularity exec -e fastqc-0.11.9.sif fastqc
singularity run -e fastqc-0.11.9.sif

Compare env command with and without -e modifier.

singularity exec fastqc-0.11.9.sif env
singularity exec -e fastqc-0.11.9.sif env

Exercise

  • Generate a Singularity image of the last samtools version

    • Consider and compare different registry sources

  • Explore the inside contents of the image

  • Execute in different ways samtools program (e. g., using fqidx option)

Singularity recipes

Docker bootstrap

BootStrap: docker
From: biocontainers/fastqc:v0.11.9_cv7

%runscript
    echo "Welcome to FastQC Image"
    fastqc --version

%post
    echo "Image built"

sudo singularity build fastqc.sif docker.singularity

Singularity advanced aspects

Sandboxing

singularity build --sandbox ./sandbox docker://ubuntu:18.04
touch sandbox/etc/myetc.conf
singularity build sandbox.sif ./sandbox

Bind paths (aka volumes)

Paths of host system mounted in the container

  • Default ones, no need to mount them explicitly (for 3.6.x): `$HOME` , `/sys:/sys` , `/proc:/proc`, `/tmp:/tmp`, `/var/tmp:/var/tmp`, `/etc/resolv.conf:/etc/resolv.conf`, `/etc/passwd:/etc/passwd`, and `$PWD` Ref

For others, need to be done explicitly (syntax: host:container)

mkdir datatest
touch datatest/testout
singularity shell -e -B ./datatest:/scratch fastqc-0.11.9.sif
> touch /scratch/testin
> exit
ls -l testdir

Exercise

Using the 2 fastq available files, process them outside and inside a mounted directory using fastqc.

Suggested solution
# Let's create a dummy directory
mkdir datatest

# Let's copy contents of testdata in that directory

singularity exec fastqc.sif fastqc datatest/*fastq.gz

# Check you have some HTMLs there. Remove them
rm datatest/*html

# Let's use shell
singularity shell fastqc.sif
> cd datatest
> fastqc *fastq.gz
> exit

# Check you have some HTMLs there. Remove them
singularity exec -B ./datatest:/scratch fastqc.sif fastqc /scratch/*fastq.gz

# What happens here!
singularity exec -B ./datatest:/scratch fastqc.sif bash -c 'fastqc /scratch/*fastq.gz'

Instances

Also know as services. Despite Docker it is still more convenient for these tasks, it allows enabling thing such as webservices (e.g., via APIs) in HPC workflows.

As a simple example, first we create a boostrapped image:

Bootstrap: docker
From: library/mariadb:10.3

%startscript
        mysqld

sudo singularity build mariadb.sif mariadb.singularity

mkdir -p testdir
mkdir -p testdir/db
mkdir -p testdir/socket

singularity exec -B ./testdir/db:/var/lib/mysql mariadb.sif mysql_install_db

singularity instance start -B ./testdir/db:/var/lib/mysql -B ./testdir/socket:/run/mysqld mariadb.sif mydb

singularity instance list

singularity exec instance://mydb mysql -uroot

singularity instance stop mydb

More information:

Singularity tips

Troubleshooting

singularity --help

Fakeroot

Singularity permissions are an evolving field. If you don’t have access to sudo, it might be worth considering using –fakeroot/-f parameter.

Singularity cache directory

$HOME/.singularity

  • It stores cached images from registries, instances, etc.

  • If problems may be a good place to clean. When running sudo, $HOME is /root.

Global singularity configuration

Normally at /etc/singularity/singularity.conf or similar (e.g preceded by /usr/local/)

  • It can only be modified by users with administration permissions

  • Worth noting bind path lines, which point default mounted directories in containers