Copyright (c) 2013-2023 Aurelien Ginolhac, UL HPC Team <[email protected]>
Through this tutorial you will learn how to use the R package {targets}: A function-oriented Make-like workflow manager.
Warning: this tutorial does not focus on the learning of R language. If you’re also looking for a good tutorial on R’s data structures you can take a look at: Hadley Wickham’s page. Another bookdown’s book is available for free: R for Data Science by Hadley Wickham, Mine Çetinkaya-Rundel & Garrett Grolemund.
Ensure you are able to connect to the UL HPC clusters
you MUST work on a computing node
# /!\ FOR ALL YOUR COMPILING BUSINESS, ENSURE YOU WORK ON A COMPUTING NODE
(access-iris)$> si -c 2 -t 1:00:00A Singularity image was prepared that contains an Ubuntu-based R 4.2.2
but with all necessary packages. Of note this was created using renv::restore(). renv helps to manage R dependency to projects.
- Once on a node, load Singularity
module load tools/Singularity
The demo repository is targets_demos.
cd $HOME
git clone --branch hpc https://gitlab.lcsb.uni.lu/aurelien.ginolhac/targets_demos.git- Check you can tart a container inside this newly fetched folder
singularity run -H /home/users/${USER}/targets_demos/ --contain \
/scratch/users/aginolhac/targets_hpc/r-targets.sif lsHere we bind as home only the targets_demos folder (specifying -H this new home and --contain to not bind the rest of your home) and list its content:
LICENSE.md README.md _targets_ds_1.R _targets_ds_2_crew.R _targets_ds_fun1.R circles ds1.Rmd ds3.Rmd lines renv.lock
R _targets.yaml _targets_ds_2.R _targets_ds_3.R _targets_packages.R data ds2.Rmd img others run.RI have followed this tutorial: R-VScode by Roland Krasser