Overview
Learning Objectives
Installing Prokka
Conda installation
conda create -n GVA-prokka -c conda-forge -c bioconda -c defaults prokka conda activate GVA-prokka
Check for correct installation and get review command line options
prokka --version prokka --listdb prokka --help
expected output
prokka 1.14.6
Looking for databases in: /work2/01821/ded/stampede2/miniconda3/envs/GVA-prokka/db
* Kingdoms: Archaea Bacteria Mitochondria Viruses
* Genera: Enterococcus Escherichia Staphylococcus
* HMMs: HAMAP
* CMs: Archaea Bacteria Viruses
help command should give list of options you are familiar with by now