susheelbhanu/gRodon

Snakefile and scripts for running gRodon

gRodon

Snakefile and scripts for running gRodon

• Purpose: To determine maximal growth rates using codon usage patterns (CUB)
• Repo: https://github.com/jlw-ecoevo/gRodon2
• Vignette: https://jlw-ecoevo.github.io/gRodon-vignette
• Updated on: 2021-10-31

Update notes

• Created two running modes: prokaryotes and eukaryotes
• Added rules for both prokaryote and eukaryotes growth rate prediction using CUB

Usage:

• Edit the config/config.yaml file to specify the steps, i.e. running mode
• Example: ["prokaryotes", "eukaryotes"]

conda activate snakemake
snakemake -s Snakefile --configfile config/config.yaml --use-conda --cores 32 -rp 

• Notes:
  • Requires snakemake >=5.32.0 to run
  • Update the following files prior to running
    • config/config.yaml: adjust paths for the individual directories
    • data/prokaryotes.txt: filenames for Prokaryote MAGs without the extension (eg: .fa or .fasta or .fna)
    • data/eukaryotes.txt: filenames for Eukaryote MAGs without the extension (eg: .fa or .fasta or .fna)