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docker-prokka

Docker Automated buil

Docker image with Prokka software.

Prokka annotates bacterial, archaeal and viral genomes
Due to licences permissions, this image does not contain:

  • SignalP (used to find signal peptide features in CDS)
    • --gram option cannot be used
  • RNAmmer (used to find ribosomal RNA features)
    • It uses Barrnap for rRNA prediction
    • --rnammer option cannot be used

Usage

You can download and run this image using the following commands:

# Get Docker image
docker pull ummidock/prokka:1.13.3-01

# Wizard annotation
docker run --rm -u $(id -u):$(id -g) -it -v /local/folder/data:/data/ ummidock/prokka:1.13.3-01 prokka --outdir /data/SAMPLE/ --force --addgenes --centre UMMI --compliant --genus Streptococcus --species agalactiae --strain SAMPLE --cpus 2 --rfam --prefix SAMPLE --locustag SAMPLEp --increment 10 /data/sample.fasta

For more examples see Prokka GitHub