Using Podman in SD Desktop

The Podman container manager is available in Ubuntu 22-based SD Desktop virtual machines. Podman is able to use Docker containers and thus it can be used to replace Docker in your SD Desktop workflows.

As SD Desktop doesn't have access to software container repositories, you must save the container you wish to use into a Docker archive file in some other environment where you have Podman or Docker. This file must then be imported to SD Desktop through SD Connect.

For example, to use Trimmomatic software in SD Desktop of CSC project project_2000123, you could use following procedure.

In a Linux server with Docker available, create a Docker container file that includes Trimmomatic. This can be done with commands:

sudo docker pull staphb/trimmomatic:latest
sudo docker images
sudo docker save -o trimmomatic.docker 932a84b67790

Here the last command uses container ID (932a84b67790) that was checked with the docker images command.

The Docker file needs to be uploaded to SD Connect from where it can be copied to a SD Desktop virtual machine. In this example the Docker file trimmomatic.docker is uploaded to SD Connect using a-put command:

a-put --sdx trimmomatic.docker -b 2000123_docker  

The command above encrypts the data (--sdx) and stores it to SD Connect bucket 2000123_docker.

To use the copied container, open or refresh the Data Gateway connection in your SD Desktop virtual machine. Then open a terminal window and copy the Docker file to the local disk of your virtual machine. Now you can load the Docker container to your Podman environment.

In the case of the Trimmomatic container you could do the container import with commands:

cp Projects/SD-Connect/project_2000123/2000123_docker/trimmomatic.docker ./
podman image load -i trimmomatic.docker
podman image list 
podman image tag 932a84b67790 trimmomatic

In SD Desktop you must always add definition --cgroup-manager cgroupfs when running a Podman container. For example, using the imported container to run Trimmomatic filtering for file /media/volume/rawdata.fastq could be now done with command:

podman --cgroup-manager cgroupfs run -v /media/volume:/media/volume trimmomatic:latest trimmomatic SE /media/volume/rawdata.fastq  /media/volume/flitered.fastq MINLEN:100

In the command above the first part of the command is the actual podman command that defines the Podman operation (run), and mounting between local and container environments (-v).

podman --cgroup-manager cgroupfs run -v /media/volume:/media/volume trimmomatic:latest

Rest of the command defines the actual trimmomatic analysis command:

trimmomatic SE /media/volume/rawdata.fastq  /media/volume/flitered.fastq MINLEN:100

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