greatfireball/ime_prokka repository overview

⁠ime_prokka

Docker image for PROKKA annotation pipeline

⁠Prerequisities

In order to run this container you'll need docker installed.

• Windows⁠
• OS X⁠
• Linux⁠

⁠Usage

The docker image provides the PROKKA⁠ software. It will run the prokka command as entrypoint. Therefore, running a container is as easy as:

docker run --rm -it greatfireball/ime_prokka --version

Just provide all required parameters via command line. Default working directory is /data. Therefore, input data should be mounted using /data volume.

Running the command to run PROKKA on its sample files in result as output folder in the current folder:

docker run --rm -it -v $PWD:/data greatfireball/ime_prokka \
   --cpus 2 \
   --outdir result \
   --prefix asm \
   /opt/prokka/test/plasmid.fna

⁠Releases

The master branch contains a rolling release. The develop branch is used for further development. Specific tags are used for different SeqFilter releases. Latest release is .

Version/Branch	Commit in Docker Repo	Image

⁠Contributing

Please read CONTRIBUTING.md⁠ for details on our code of conduct, and the process for submitting pull requests to us.

⁠Author

• Frank Förster - Initial work - greatfireball⁠

See also the list of contributors⁠ who participated in this project.

⁠License

This project is licensed under the MIT License - see the LICENSE.md⁠ file for details.