How do I run pgsc_calc in an offline environment?#

pgsc_calc has been deployed on secure platforms like Trusted Research Environments (TREs). Running pgsc_calc is a little bit more difficult in this case. The basic set up approach is to:

Download containers
Download reference data
Download scoring files

And transfer everything to your offline environment.

This guide assumes you’ve set up pgsc_calc and tested it in an online environment first.

Every computing environment has different quirks and it can be difficult to get everything working correctly. Please feel free to open a discussion on Github if you are having problems and we’ll try our best to help you.

Preload container images#

Docker#

Pull and save the docker images to local tar files in an online environment:

$ cd /path/to/pgsc_calc
$ git grep 'ext.docker*' conf/modules.config | cut -f 2 -d '=' | xargs -L 2 echo | tr -d ' ' > images.txt
$ cat images.txt | xargs -I {} sh -c 'docker pull --platform linux/amd64 "$1"' - {}
$ mkdir -p docker/
$ cat images.txt | xargs -I {} sh -c 'docker save "$1" > docker/$(basename "$1").tar' - {}

Tar files will have been saved to the docker/ directory. Transfer this directory and load the container tars in the offline environment:

$ find docker -name '*.tar'
$ find docker/ -name '*.tar' -exec sh -c 'docker load < {}' \;

Singularity#

Set NXF_SINGULARITY_CACHEDIR to the directory you want containers to download to:

$ cd /path/to/pgsc_calc
$ export NXF_SINGULARITY_CACHEDIR=path/to/containers

Then pull the images to the directory:

$ mkdir -p $NXF_SINGULARITY_CACHEDIR
$ git grep 'ext.singularity*' conf/modules.config | cut -f 2 -d '=' | xargs -L 2 echo | tr -d ' ' > singularity_images.txt
$ cat singularity_images.txt | sed 's/oras:\/\///;s/https:\/\///;s/\//-/g;s/$/.img/;s/:/-/' > singularity_image_paths.txt
$ paste -d '\n'singularity_image_paths.txt singularity_images.txt | xargs -L 2 sh -c 'singularity pull --disable-cache --dir $NXF_SINGULARITY_CACHEDIR $0 $1'

And transfer the directory to your offline environment.

Warning

Remember to set NXF_SINGULARITY_CACHEDIR to the directory that contains the downloaded containers on your offline system whenever you run pgsc_calc, e.g.:

$ export NXF_SINGULARITY_CACHEDIR=path/to/containers
$ nextflow run main.nf -profile singularity ...

Download reference data#

Some small reference data is needed to run the calculator:

–hg19_chain https://hgdownload.cse.ucsc.edu/goldenpath/hg19/liftOver/hg19ToHg38.over.chain.gz
–hg38_chain https://hgdownload.soe.ucsc.edu/goldenPath/hg38/liftOver/hg38ToHg19.over.chain.gz

To do ancestry-based score normalisation you’ll need to download the reference panel too. See Reporting and adjusting PGS in the context of genetic ancestry.

Download scoring files#

It’s best to manually download scoring files from the PGS Catalog in the correct genome build. Using PGS001229 as an example:

https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001229/ScoringFiles/

$ PGS001229/ScoringFiles
  ├── Harmonized
  │   ├── PGS001229_hmPOS_GRCh37.txt.gz <-- the file you want
  │   ├── PGS001229_hmPOS_GRCh37.txt.gz.md5
  │   ├── PGS001229_hmPOS_GRCh38.txt.gz <-- or perhaps this one!
  │   └── PGS001229_hmPOS_GRCh38.txt.gz.md5
  ├── PGS001229.txt.gz
  ├── PGS001229.txt.gz.md5
  └── archived_versions

These files can be transferred to the offline environment and provided to the workflow using the --scorefile parameter.

Tip

If you’re using multiple scoring files you must use quotes e.g. --scorefile "path/to/scorefiles/PGS*.txt.gz"

Contents

About the project

Useful links

How do I run pgsc_calc in an offline environment?