Containers and Workflows in Bioinformatics

We have earlier converted Docker images from registries to corresponding singularity images in the previous tutorials. Sometimes, the images may not be readily available in image registries for our purpose. In that case, we have to either modify an existing docker image or build a new one. Unfortunately, the docker-related operations can only be done on our local machines or any host machine where we have privileged root access. This tutorial explains how to build a singularity image from a local docker image in play-with-docker environment.

Expected outcome of this tutorial:

After this tutorial, you will learn to:

• Save a docker image locally
• Launch a singularity container from a local docker image

Converting a local docker image to singularity

1. Let’s use the same trimmomatic software example we have used in the previous tutorial. In PWD terminal, run the following command to pull an image:

    docker pull quay.io/biocontainers/trimmomatic:0.32--hdfd78af_4
   

   In a real-world use case, you may want to modify the image pulled from registries or even build new one on your local machine to meet your needs.

2. Once an image is pulled or built on your local machine, the image is stored in local registry (usually at /var/lib/docker) on host machines. In order to find the stored docker images, use docker images command.

   docker images
   

   From the above command, you need to find an image ID of trimmomatic image to save it locally.

3. Create a tarball of the Docker image (with image id as cc8b303fee58) using the docker save command as below:

   docker save cc8b303fee58 -o trimmomatic_image.tar  # in this case image_id is : cc8b303fee58
   ls -l  trimmomatic_image.tar  # to see the local copy of image tarball
   

4. Copy the image tarball from PWD to your *scratch folder on Puhti

   scp trimmomatic_image.tar YOURCSCUSERNAME@puhti.csc.fi:/scratch/project_xxx/YOURCSCUSERNAME
   

5. Build Singularity image from the tarball.

    cd /scratch/project_xxxx/YOURCSCUSERNAME  # replace `project_xxxx` with a valid project number 
    singularity build local_trimmomatic_image.sif docker-archive://trimmomatic_image.tar
   

6. Launch singularity container and check if you can get a command-line help for trimmomatic software

   singularity exec local_trimmomatic_image.sif trimmomatic --help
   

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