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.

Software#

Note

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

Docker#

quay.io/biocontainers/plink2:2.00a3.3--hb2a7ceb_0
quay.io/biocontainers/multiqc:1.13--pyhdfd78af_0
dockerhub.ebi.ac.uk/gdp-public/pgsc_calc/pgscatalog_utils:${params.platform}-0.3.1
dockerhub.ebi.ac.uk/gdp-public/pgsc_calc/report:${params.platform}-2.14

Choosing a container architecture#

Note

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#

https://depot.galaxyproject.org/singularity/multiqc:1.13--pyhdfd78af_0
https://depot.galaxyproject.org/singularity/plink2:2.00a3.3--hb2a7ceb_0
oras://dockerhub.ebi.ac.uk/gdp-public/pgsc_calc/singularity/pgscatalog_utils:amd64-0.3.1
oras://dockerhub.ebi.ac.uk/gdp-public/pgsc_calc/singularity/report:2.14

Note

Singularity images are built from the docker images.

To download singularity images run:

$ singularity pull <url>

Warning

We only build singularity images for amd64