Reference: container images

The recommended way of running pgsc_calc requires downloading and running container images that we have built and hosted in publicly available container registries. The container images contain software that we need to calculate scores. The workflow normally automatically downloads and runs the required containers. 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

• Up to 6 containers are currently required to run pgsc_calc

• Only 4 containers are required if you choose not to run ancestry assignment

Minimum required software:

• plink2 2.00a3.3

  • Used to work with target genomes and to calculate scores

• pyyaml

  • Used to collect and report software versions used across the pipeline

• pgscatalog_utils

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

• report

  • Contains publishing tools to produce the summary report

Ancestry assignment software:

• fraposa_pgsc

  • A method of robustly predicting the ancestry of target genomes by projecting them into a PCA space derived from reference genomes

• zstd

  • A fast lossless compression algorithm, used to compress and decompress reference data, and natively supported by plink2

Downloading containers

Production versions of docker and singularity containers can be downloaded from the PGS Catalog Github package registry.

Singularity images have -singularity appended to container tags.

Docker images support linux/amd64 and linux/arm64 platforms.

Versions

Information about the specific versions that pgsc_calc is using is stored in the conf/modules.config file:

    
    withLabel: pgscatalog_utils {
        ext.conda = "$projectDir/environments/pgscatalog_utils/environment.yml"
        ext.docker = 'ghcr.io/pgscatalog/pgscatalog_utils'
        ext.singularity = 'oras://ghcr.io/pgscatalog/pgscatalog_utils'
        ext.docker_version = ':v0.4.2'
        ext.singularity_version = ':v0.4.2-singularity'
    }

    withLabel: plink2 {
        ext.conda = "bioconda::plink2==2.00a3.3"
        ext.docker = 'ghcr.io/pgscatalog/plink2'
        ext.singularity = 'oras://ghcr.io/pgscatalog/plink2'
        ext.docker_version = ':2.00a3.3'
        ext.singularity_version = ':2.00a3.3-singularity'
    }

    withLabel: zstd {
        ext.conda = "$projectDir/environments/zstd/environment.yml"
        ext.singularity = 'oras://dockerhub.ebi.ac.uk/gdp-public/pgsc_calc/singularity/zstd'
        ext.singularity_version = ':amd64-1.4.8'
        ext.docker = 'dockerhub.ebi.ac.uk/gdp-public/pgsc_calc/zstd'
        ext.docker_version = ':1.4.8'
    }

    withLabel: report {
        ext.conda = "$projectDir/environments/report/environment.yml"
        ext.singularity = 'oras://dockerhub.ebi.ac.uk/gdp-public/pgsc_calc/singularity/report'
        ext.singularity_version = ':2.0'
        ext.docker = 'dockerhub.ebi.ac.uk/gdp-public/pgsc_calc/report'
        ext.docker_version = ':2.0'
    }

    withLabel: pyyaml {
        ext.conda = "conda-forge::pyyaml==6.0"
        ext.singularity = 'oras://ghcr.io/pgscatalog/pyyaml'
        ext.singularity_version = ':6.0-singularity'
        ext.docker = 'ghcr.io/pgscatalog/pyyaml'
        ext.docker_version = ':6.0'
    }

    withLabel: fraposa {
        ext.conda = "$projectDir/environments/fraposa/environment.yml"
        ext.singularity = 'oras://ghcr.io/pgscatalog/fraposa_pgsc'
        ext.singularity_version = ':v0.1.0-singularity'
        ext.docker = 'ghcr.io/pgscatalog/fraposa_pgsc'
        ext.docker_version = ':v0.1.0'
    }

    

Software versions will change across different releases of pgsc_calc. This information is also included in the output path results/pipeline_info/versions.yml by default.