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.