oggmap docker image quick start and additional notes

In this documentation, we provide example commands for our oggmap docker image below. But we are not aiming to provide detailed information about general docker usage. We highly recommend learning about docker if you are not familiar with it, and make sure you have adequate knowledge about docker prior to start oggmap analysis with docker.

Quick start - Docker - bash

1. Download oggmap docker image from docker Hub.

docker pull kkuweb/oggmap_ubuntu:latest

2. Make docker container and start running it.

• To access files smoothly, we can use bind mount. Here, we will mount the data_folder, a directory in your local machine.

mkdir data_folder # Create data folder in your local environment.
docker run -dit \
  --name oggmap_container \
  -v $(pwd)/data_folder:/root/data_folder \
  oggmap_ubuntu:latest

3. Enter the docker container.

docker container exec -it oggmap_container bash

4. In the docker container environment, start using oggmap bash scripts.

cd
cd data_folder
oggmap -h
oggmap qlin -q "Arabidopsis thaliana"

Quick start - Docker - jupyter

1. Download oggmap docker image from docker Hub.

docker pull kkuweb/oggmap_ubuntu:latest

2. Make docker container and start running it.

• As we recommend using jupyter notebook (or jupyter lab), we need to set up port. Here, we connect docker container port 8888 with local host port 8888.

• To access files smoothly, we can use bind mount. Here, we will mount the data_folder, a directory in your local machine.

mkdir data_folder # Create data folder in your local environment.
docker run -dit \
  --name oggmap_container \
  -p 8888:8888 \
  -v $(pwd)/data_folder:/mnt/data_folder \
  kkuweb/oggmap_ubuntu:latest

3. Enter the docker container.

docker container exec -it oggmap_container bash

4. In the docker container environment, start jupyter notebook as follows.

cd /mnt/data_folder
jupyter notebook --port=8888 --ip=0.0.0.0 --allow-root --no-browser --notebook-dir=/mnt/data_folder

After starting jupyter, please open your browser and enter http://localhost:8888 to access jupyter notebook running in the docker container. You need to enter a token to access jupyter. The token can be found in your terminal running jupyter notebook.

5. Start using oggmap from jupyter using the oggmap_env kernel.

from oggmap import qlin
qlin.get_qtid(q='Arabidopsis thaliana', dbname='taxadb.sqlite')

Docker image build information

We built our docker image using Dockerfile automatic build function. The Dockerfile is available here. You can modify it to create custom docker image by yourself. If you make custom environment, please do so on your responsibility.