README

This is a Docker image for Regulatory Genomics Toolbox. We use Jupyter data science notebook as the base image and pip/conda installed the relevant packages.

Build the Docker image

To build the Docker image, run the command

docker build .

For convenience, the Docker image can be found in Dockerhub.

To pull from Dockerhub, you can simply run:

docker pull yosuketanigawa/rgt

Set up the reference dataset

mount_dir=@@@ # specify the directory that you'd like to mount for the analysis with RGT
rgtdata_dir=@@@ # specify the directory where you installed your local copy of the reference data for RGT

Download the genomic reference data

docker run --rm -w /home/jovyan/rgtdata --user=$(id -u):$(id -g) -e NB_USER=jovyan -e NB_UID=$(id -u) -e NB_GID=$(id -g) --mount type=bind,src=${rgtdata_dir},dst=/home/jovyan/rgtdata yosuketanigawa/rgt python setupGenomicData.py --all

Download the logo data

docker run --rm -w /home/jovyan/rgtdata --user=$(id -u):$(id -g) -e NB_USER=jovyan -e NB_UID=$(id -u) -e NB_GID=$(id -g) --mount type=bind,src=${rgtdata_dir},dst=/home/jovyan/rgtdata yosuketanigawa/rgt python setupLogoData.py --all

How to use the docker image

Here we show some example use cases:

Running motif analysis

docker run --rm -w $(readlink -f $(pwd)) --user=$(id -u):$(id -g) -e NB_USER=jovyan -e NB_UID=$(id -u) -e NB_GID=$(id -g) --mount type=bind,src=${mount_dir},dst=${mount_dir} --mount type=bind,src=${rgtdata_dir},dst=/home/jovyan/rgtdata yosuketanigawa/rgt rgt-motifanalysis

Acknowledgement