uc-CWR

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-v0.18.07385641ux-x64.tar.gz
   
   tar -xvf hq-v0.18.0-linux-x64.tar.gz
   
   rm hq-v0.18.0-linux-x64.tar.gz  
   

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

   sbatch submit_modgp_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