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Singularity version .In this case, start with a machine (e.g., your personal computer) with Docker installed.Use docker2singularity tocreate a singularity image.You will need an active internet connection and some time.

Setting up a functional execution framework with Singularity might be tricky in someHPC systems.Please make sure you have read the relevant documentation of Singularity, and checked all the defaults and configuration in yoursystem.The next step is checking the environment and access to fMRIPrep resources, usingsingularity shell.

Singularity executes a container from a Singularity container image either created by the user or downloaded from Singularity Library , and can also import and execute Docker container images, either directly uploaded by the user, or downloaded from Docker Hub

Singularity images may have a run script (Docker: ENTRYPOINT) that is executed when the singularity run command is used. To see the run script defined by the container (if any), use the singularity inspect command:

The output above shows that in the aforementioned Docker image for the R programming language retrieved from Docker Hub, singularity run r-base.img will run R interactively in the container environment. Your home directory is automatically mounted in the container, so any files therein can be accessed (and R packages installed within the container, as illustrated in the example below):

A container image can contain many executables / scripts. The singularity exec command can be used to select which program to run in the container. For example, to run a simple R script using the Rscript command in the container, prefix the Rscript command with singularity exec r-base.img:

singularity shell starts an interactive shell within the container image, allowing you to inspect files (and execute programs) within the container. For example, here we see that the r-base.img container image was created using Debian Linux as the base operating system:

If you're using Singularity, the nf-core download command can also fetch the required Singularity container images for you.To do this, select singularity in the prompt or specify --container singularity in the command.Your archive / target output directory will then include three folders: workflow, configs and also singularity-containers.

This tells Nextflow to use the singularity-containers directory relative to the workflow for the singularity image cache directory.All images should be downloaded there, so Nextflow will use them instead of trying to pull from the internet.

If found, the tool will fetch the Singularity images to this directory first before copying to the target output archive / directory.Any images previously fetched will be found there and copied directly - this includes images that may be shared with other pipelines or previous pipeline version downloads or download attempts.

If you are running the download on the same system where you will be running the pipeline (eg. a shared filesystem where Nextflow won't have an internet connection at a later date), you can choose to only use the cache via a prompt or cli options --singularity-cache-only / --singularity-cache-copy.

This instructs nf-core download to fetch all Singularity images to the $NXF_SINGULARITY_CACHEDIR directory but does not copy them to the workflow archive / directory.The workflow config file is not edited. This means that when you later run the workflow, Nextflow will just use the cache folder directly.

Some DSL2 modules have container addresses for docker (eg. quay.io/biocontainers/fastqc:0.11.9--0) and also URLs for direct downloads of a Singularity continaer (eg. :0.11.9--0).Where both are found, the download URL is preferred.

We also need to initialise your environment to make Singularity available. NeSI maintains up-to-date versions of Singularity as software modules on Mahuika. Load the latest Singularity and check the version. Note that the singularity command includes extensive self-documentation::

For the ERNZ20 tutorial we have prepared some of the bigger images to be downloaded in a specific directory - /nesi/nobackup/nesi99991/ernz20-containers/demos/sif/. Create the following symbolic link to be able to use them. Normally downloading the required images will take up to an hour.

Being able to specify download locations for the container images allows you to keep your local set of images organised and tidy, by making use of a directory tree. It also allows for easy sharing of images within your team in a shared resource.

The default directory location for the image cache is $HOME/.singularity/cache. This location can be inconvenient in shared resources such as HPC centres, where often the disk quota for the home directory is limited. You can redefine the path to the cache dir by setting the variable SINGULARITY_CACHEDIR.

The singularity containers can be also be used in combination with our Transparent Singularity Tool tool, that wraps the executables inside a container to make them easily available for pipelines. More information can be found here:

Although the Singularity research development kit (RDK) is available for download, it is not technically open source. The source code is distributed under the terms of the restrictive Microsoft Research License rather than one of Microsoft's two OSI-approved open source licenses. Singularity can only be used for noncommercial academic use, and the license for the Singularity RDK explicitly stipulates that you can't use the included compilers to develop production software. Developers who are interested in open source managed code kernels that can be used in commercial and production environments might want to look at the SharpOS and Cosmos projects, which we wrote about early last month.

The system administrator can also define what is added to a container. This is important on campus HPC systems that often have a /scratch or /xdisk directory structure. By editing the /etc/singularity/singularity.conf a new path can be added to the system containers.

At the time of this writing, no suitable version of Singularity is available as system package for Ubuntu (the most popular Linux distro). Therefore we decided to make our own packages for users who need a simple way to install Singularity. Look in the following table for a suitable package for your Linux distro. If found, download it and install it, either using a graphical tool, or the following commandline:

Using singularity on Windows works only with Windows 10 and requires a recent technology (deployed in late summer 2020, your system must have been updated afterward) allowing to run Linux in Windows. This technology, called Windows Subsystem For Linux 2 (WSL2) must be enabled on the system. Then a Linux distro must be installed from the Microsoft Store. Finally an X Windows server must be installed and started.

Docker images are not secure because they provide a means to gain root access to the system they are running on. For this reason Docker is not available on the Princeton Research Computing clusters (neither is nvidia-docker). This is not a problem because we offer Singularity which is an alternative to Docker that is both secure and designed for high-performance computing. Singularity is compatible with all Docker images and it can be used with GPUs and MPI applications. Learn about the differences between virtual machines, Docker and Singularity. Be aware of Apptainer by reading about the history of singularity.

Working with Singularity images requires lots of storage space. By default Singularity will use /.singularity as a cache directory which can cause you to go over your /home quota. Consider adding these environment variables to your /.bashrc file:

Singularity images are made from scratch using a definition file which is a text file that specifies the base image, the software to be installed and other information. See the documentation for singularity build.