chrishah/metabeat repository overview

metaBarcoding and Environmental DNA analyses tool

More details about the pipeline can be found on our Github page⁠.

We build on the docker image for Reprophylo⁠ running Ubuntu 14.04.

CONTACT: [email protected]⁠

Run the metaBEAT script in the container (you can process data in you current working directory or subdirectories of it):

sudo docker run --rm --net=host --name metaBEAT -v $(pwd):/home/working chrishah/metabeat metaBEAT_global.py -h

In a terminal window, mount the docker container to your current working directory and enter the self contained environment using a shell:

sudo docker run -i -t --net=host --name metaBEAT -v $(pwd):/home/working chrishah/metabeat /bin/bash

Or access the container via a Jupyter notebook, by simply running the start_metaBEAT_nb providing the full path to your desired mounting point to the script, e.g.:

./start_metaBEAT_nb $(pwd) --xt

This will open a Jupyter notebook in a new tab in your default browser. First it will notify you that your connection is not private. Click on Advanced on the bottom left and proceed to local host (unsafe). Then you will be asked to provide a password, which is simply password. Entering the password correctly will now open the Jupyter notebook and you are good to go.

Once you are done, you should stop the container by simply running:

stop_metaBEAT_nb

Within the environment you can then execute the scripts that come with metaBEAT, e.g.:

metaBEAT_global.py