To get started, you will need to go through the following steps.
Jupyter notebooks needed for this workshop are provided in the GitHub repository: https://github.com/bioinfodlsu/metagenomics-workshop. Click the (green) Code button to download zip. Unzip, and place the metagenomics-workshop-main folder at your preferred location.
A dataset containing pre-downloaded reference databases and some metagenomic samples can be downloaded from here.
Download, unzip, and place the data folder inside metagenomics-workshop-main folder.
If there are issues with downloading, a copy of the dataset will provided via a flash drive at the workshop site.
Skip this step if you already have Docker installed on your system. Instruction to install Docker is available at https://docs.docker.com/desktop.
To resolve software dependency issues, we have provided a Docker image containing all software tools required for this workshop here.
Ensure you are running Docker Desktop/Engine. In the Command Prompt/Terminal, execute the following to download/pull the Docker image:
docker pull ghcr.io/bioinfodlsu/metagenomics-workshop/deploy:latest
In the Command Prompt/Terminal, launch a Docker container by executing the following, replacing path_to_metagenomics-workshop-main with the actual path on your system. If you are at the top-level of the metagenomics-workshop-main folder, the path is simply a dot ..
docker run -it --rm -p 8888:8888 -v path_to_metagenomics-workshop-main:/home/jovyan/work ghcr.io/bioinfodlsu/metagenomics-workshop/deploy:latest
Once the container is running, a link to the Jupyter Lab interface, including the authentication token (e.g., http://127.0.0.1:8888/?token=your_token), will appear in the terminal or command prompt after starting the container. Copy and paste this link into your browser.
A JupyterLab interface should appear. On the left pane is the file browser. If you click on the folder `work', you should be able to see the raw version of this page as well as other notebooks and pages.