add pgge module and replace Singularity based deployment

[DininduSenanayake]

add pgge module and replace Singularity based deployment

[DininduSenanayake]

@JSBoey Let's address pgge deployment issues here. Container based module pgge/.2021-container (hidden) is available and I will run through the related section on material now

[JSBoey]

Check that pgge is accessing the container version of R and related packages. I am unsure if it is reading my account's R setup.

[DininduSenanayake]

pgge/.2021-container is not reading R library. It is definitely there as calling the container directly confirms it

$ module load Singularity/3.11.3 
$ singularity shell /opt/nesi/containers/pgge/pgge.simg 
Singularity> R

> library(tidyverse)
-- Attaching packages --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- tidyverse 1.3.0 --
v ggplot2 3.3.3     v purrr   0.3.4
v tibble  3.1.0     v dplyr   1.0.5
v tidyr   1.1.3     v stringr 1.4.0
v readr   1.4.0     v forcats 0.5.1
-- Conflicts ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ tidyverse_conflicts() --
x dplyr::filter() masks stats::filter()
x dplyr::lag()    masks stats::lag()

I will fix it now by adding the corresponding library paths to the module file or something along those lines

[DininduSenanayake]

@JSBoey This is fixed now and the new module is visible to everyone. (different name as I have dropped the container altogether and rebuilt the module with a custom conda environment)

$ module load pgge/2021-Miniconda3 

$ R

R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-conda-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

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Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

[Previously saved workspace restored]

> library(tidyverse)
── Attaching packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────── tidyverse 1.3.0 ──
✔ ggplot2 3.3.6      ✔ purrr   0.3.4 
✔ tibble  3.1.8      ✔ dplyr   1.0.10
✔ tidyr   1.2.1      ✔ stringr 1.4.1 
✔ readr   2.1.2      ✔ forcats 0.5.2 
── Conflicts ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::filter() masks stats::filter()
✖ dplyr::lag()    masks stats::lag()
Warning messages:
1: package ‘ggplot2’ was built under R version 4.0.5 
2: package ‘tibble’ was built under R version 4.0.5 
3: package ‘tidyr’ was built under R version 4.0.5 
4: package ‘readr’ was built under R version 4.0.5 
5: package ‘dplyr’ was built under R version 4.0.5 
6: package ‘stringr’ was built under R version 4.0.5 
7: package ‘forcats’ was built under R version 4.0.5