Reference: container images
Contents
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 themultiqc
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
andamd64
architectures, because multi-arch builds caused some problems with our container registryBiocontainers 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