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Annotation with Prokka and intro of Roary

Note 1: replace whatever is between <> with the proper value. For example, in "Organize the data" <your_species_name>, write the species name you selected (something like campylobacter_jejuni).
Note 2: if the VM has 16 CPUs, use 16 in CPUs/threads instead of 8.
Note 3: do the steps bellow for the bacteria species of your choise. Streptococcus agalactiae is used as example.

# Before start, make sure Prokka image is already in the VM
sudo service docker restart
docker pull ummidock/prokka:1.12
# Annotate the genomes
## Create a folder to store the annotations
mkdir /media/volume/annotation
## Prepare folder to run Prokka
mkdir /media/volume/annotation/<your_species_name>
mkdir /media/volume/annotation/<your_species_name>/prokka

# Create a folder for Streptococcus agalactiae example
mkdir /media/volume/annotation/streptococcus_agalactiae_example
mkdir /media/volume/annotation/streptococcus_agalactiae_example/prokka
# Run Prokka
## Copy genomes folders to extra volume to Prokka folder to map into Docker container
cp -r ~/genomes/streptococcus_agalactiae_example/all_assemblies/ /media/volume/annotation/streptococcus_agalactiae_example/prokka/
## Run Prokka
ls /media/volume/annotation/streptococcus_agalactiae_example/prokka/all_assemblies/* | \
      parallel --jobs 8 'docker run --rm -u $(id -u):$(id -g) -v /media/volume/annotation/streptococcus_agalactiae_example/prokka/:/data/ ummidock/prokka:1.12 prokka --outdir /data/$(echo {/} | cut -d "." -f 1) --force --centre MGMC --genus Streptococcus --species agalactiae --strain $(echo {/} | cut -d "." -f 1) --cpus 1 --prefix $(echo {/} | cut -d "." -f 1) --locustag $(echo {/} | cut -d "." -f 1)p --addgenes --usegenus --rfam --increment 10 --mincontiglen 1 --gcode 1 --kingdom Bacteria /data/all_assemblies/{/}'