Singularity

Bootstrap: library
From: richelbilderbeek/default/gcaer:0.6.6

%post
    # Update prerequisites
    Rscript -e 'remotes::install_github("richelbilderbeek/plinkr")'
    Rscript -e 'remotes::install_github("richelbilderbeek/ormr")'
    Rscript -e 'remotes::install_github("richelbilderbeek/gcaer")'
    Rscript -e 'remotes::install_github("richelbilderbeek/uppmaxr")'
    
    # The package it is about
    Rscript -e 'remotes::install_github("richelbilderbeek/nsphs_ml_qt")'

%runscript
echo "'nsphs_ml_qt.sif' running with arguments '$@'"
exec "$@"

%test
    Rscript -e 'gcaer::gcaer_report(gcae_options = gcaer::create_gcae_options(gcae_folder = "/opt/gcae_richel", ormr_folder_name = "python3"))'

%help

This container has the R package 'nsphs_ml_qt' and GCAE installed,
including the needed Python packages.

To make the container run a script called, e.g. `script.R`, do:

```
singularity run nsphs_ml_qt.sif Rscript script.R
```

NOTE: The GCAE scripts can be found at '/opt/GenoCAE',
which is the same as the `gcae_folder` parameter.

NOTE: The installed Python packages can be found at '/opt/ormr_gcaer',
which is the same as the `ormr_folder_name` parameter.

NOTE: Due to this, within your scripts,
set `gcae_options` to `create_gcae_options(gcae_folder = "/opt/GenoCAE", ormr_folder_name = "/opt/ormr_gcaer")`,
for example:

```
# library(nsphs_ml_qt)
# gcae_options <- create_gcae_options(gcae_folder = "/opt/GenoCAE", ormr_folder_name = "/opt/ormr_gcaer")
# run_gcae(args = "--help", gcae_options = gcae_options)
```

%labels

    AUTHOR Richel J.C. Bilderbeek

    NAME nsphs_ml_qt

    DESCRIPTION The nsphs_ml_qt R package, with PLINK and Python packages installed

    USAGE Run as usual, i.e. `singularity run nsphs_ml_qt.sif Rscript script.R`

    URL https://github.com/richelbilderbeek/nsphs_ml_qt

    VERSION 0.4