Reference: container images#

The recommended way of running pgsc_calc requires downloading and running container images that we have built and hosted. The container images contain software that we need to calculate scores. Below is a list of container images for reference, which might be helpful if you’d like to download and inspect them manually.



4 containers are currently required to run pgsc_calc

Some containers are made by Biocontainers, and hosted on their container registry.

  • plink2 2.00a3.3
    • Used to work with target genomes and to calculate scores

  • multiqc
    • Used to collect and report software versions (only the pyyaml library is used from the multiqc image)

Other containers are hosted on a Gitlab container registry:

  • pgscatalog_utils
    • A collection of useful tools for working with PGS Catalog data

  • report
    • Contains R, RMarkdown, and the tidyverse to produce the summary report


Choosing a container architecture#


Remember to replace ${params.platform} with amd64 or arm64 in the image tag

  • We build separate docker images for arm64 and amd64 architectures, because multi-arch builds caused some problems with our container registry

  • Biocontainers and Bioconda currently only support amd64, so they’re not tagged with an architecture



Singularity images are built from the docker images.

To download singularity images run:

$ singularity pull <url>


We only build singularity images for amd64