pseudogene/contiguator repository overview

⁠pseudogene / contiguator

⁠Short Description

A bacterial genomes finishing tool for structural insights on draft genomes - Now in a Docker

⁠Disclamer

CONTIGuator is no longer actively maintained (except for small bugfixes and requests)! Contiguator's authors strongly suggest to use Medusa⁠ instead

⁠Full Description

Supported tags and respective Dockerfile links

• 2.7.5, latest (Dockerfile⁠)

For more information about this image and its history, please see the relevant manifest file. This image is updated via pull requests to the contiguator GitHub repo⁠.

⁠What is STACKS?

CONTIGuator⁠ is a bacterial genomes finishing tool for structural insights on draft genomes. CONTIGuator is developed by Florence computational biology group⁠.

⁠How to use this image.

For CONTIGuator run through the command line interface (CLI) allowing the deployment on Cloud, Cluster and docker Swamp.

By default the path is /data, to import and export the result of your analyse you need to link the folder we your data are to the docker /data folder by user -v <USERFOLDER>:/data.

$ docker run -it --rm -v /export:/data pseudogene/contiguator:latest \
       python /usr/local/bin/CONTIGuator.py -c "/data/contig.fasta" -r "/data/reference.fasta" -o "/data/output"

⁠Rebuild it yourself

git clone https://github.com/pseudogene/contiguators.git
cd contiguator
docker build --rm=true -t contiguator:latest -t contiguator:2.7.5 .
cd ..

⁠Colophon

Please see the Docker⁠ installation documentation for details on how to upgrade your Docker daemon.

⁠User Feedback Documentation

Be sure to familiarise yourself with the repository's README.md⁠ file before attempting a pull request.

⁠Issues

If you have any problems with or questions about this docker image, please contact us through a GitHub issue⁠. Any issue related to CONTIGuator itself must be done directly with CONTIGuator developers⁠ or via the CONTIGuator-user mailing list⁠.

⁠Contributing

You are invited to contribute new features, fixes, or updates, large or small; we are always thrilled to receive pull requests, and do our best to process them as fast as we can.

Before you start to code, we recommend discussing your plans through a GitHub issue⁠, especially for more ambitious contributions. This gives other contributors a chance to point you in the right direction, give you feedback on your design, and help you find out if someone else is working on the same thing.