- Clone this directory and PanPhlAn into a local folder:
git clone https://github.com/zhaoc1/pangenome-snakemake.git my_pangenome_project
cd my_pangenome_project
hg clone https://bitbucket.org/CibioCM/panphlan local/panphlan- Creat a new Conda environment (assumes you have Miniconda)
conda create -n my_pan --file=conda-requirements.txt --quiet --yes- Manually doanload reference genomes and clean up names
snakemake clean_names- Run Prokka to get Roary compatible features files
snakemake _all_prokka- Collect GFF files into gffs/
mkdir prokka_gffs
cp fnas/prokka_*/*.gff prokka_gffssnakemake run_roarysnakemake visualize_roary