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BioDT / uc-CWR

The code base for the Crop-Wild-Relative (CWR) use-case led by UiO
MIT License
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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

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

    sbatch submit_modgp.lumi.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