diff --git a/docs/how-to/offline.rst b/docs/how-to/offline.rst index 3fb78e25..e26ead9e 100644 --- a/docs/how-to/offline.rst +++ b/docs/how-to/offline.rst @@ -7,9 +7,10 @@ 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: -1. Download containers -2. Download reference data -3. Download scoring files +1. Set up Nextflow +2. Download containers +3. Download reference data +4. Download scoring files And transfer everything to your offline environment. @@ -22,6 +23,41 @@ if you are having problems and we'll try our best to help you. .. _open a discussion on Github: https://github.com/PGScatalog/pgsc_calc/discussions +Set up Nextflow +---------------- + +From the Nextflow documentation for `offline usage `_: + +1. Run the test profile of the calculator with ``nextflow run pgscatalog/pgsc_calc -r test,`` + +.. tip:: + + It doesn't matter if the profile you use on your computer with internet access is different to the profile you use in the airlocked environment. + + The important thing is that Nextflow automatically configures itself using an internet connection. + +2. Transfer the Nextflow binary and ``$NXF_HOME/.nextflow`` directory to your airlocked environment + +.. tip:: + + ``$NXF_HOME`` is ``$HOME`` by default, so the directory is probably ``~/.nextflow`` + +.. warning:: + + Make sure the transfer the Nextflow binary even if the airlocked environment already has Nextflow installed. It's important that the versions match across both environments. + +3. Remember to always set the environment variable ``NXF_OFFLINE='true'`` in the offline environment + + +.. tip:: + + You shouldn't need to: + + 1. Edit any Nextflow configuration files + 2. Manually download any plugins + + Unless you want to use a special plugin in the airlocked environment + Preload container images ------------------------