uc-CWR

Initial setup

1. Create a file R_scripts/SHARED-APICredentials.R. You can use the example file as a template. Insert your CDS API key and GBIF credentials in this file.

ModGP on Rstudio

1. Source ModGP_MASTER.R and change SPECIES argument at line 19 to execute ModGP pipeline for a specific genus.

ModGP on LUMI with Hyperqueue

1. Install HyperQueue:

   wget https://github.com/It4innovations/hyperqueue/releases/download/v0.18.0/hq-v0.18.0-linux-x64.tar.gz
   tar -xvf hq-v0.18.0-linux-x64.tar.gz
   rm hq-v0.18.0-linux-x64.tar.gz
   

2. Fetch the container:

   singularity pull --disable-cache docker://ghcr.io/biodt/cwr:0.5.3
   

3. Submit calculation job for a desired species (e.g. Lathyrus):

   sbatch submit_modgp_prep_lumi.sh Lathyrus
   sbatch submit_modgp_exec_lumi_HQ.sh Lathyrus
   

CAPFITOGEN demo

See documentation.

1. Download CAPFITOGEN3.zip from here and extract it to the project root.

2. Download rdatamaps/world/20x20 directory from here and extract it to CAPFITOGEN3/rdatamaps/world/20x20.

3. Run on LUMI: obtain interactive session: srun -p small --nodes=1 --ntasks-per-node=1 --mem=8G -t 4:00:00 --pty bash and execute the workflow: singularity run --bind $PWD cwr_0.2.0.sif capfitogen.R

Related publication

Chala D, Kusch E, Weiland C, Andrew C, Grieb J, Rossi T, Martinovic T, Endresen D (2024) Prototype biodiversity digital twin: crop wild relatives genetic resources for food security. Research Ideas and Outcomes 10: e125192. https://doi.org/10.3897/rio.10.e125192

Archived at Zenodo