From 94a31f1d3b3dffe1b27ca54e4382d20036257968 Mon Sep 17 00:00:00 2001 From: Daphne Go <77186592+daphnejanelyn@users.noreply.github.com> Date: Thu, 2 Jan 2025 08:59:24 +0800 Subject: [PATCH 1/2] Update README.md with new image --- README.md | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/README.md b/README.md index be1b8bb..e30420a 100644 --- a/README.md +++ b/README.md @@ -34,7 +34,7 @@ Note: Make sure you are running Docker Desktop or started your docker engine bef First, you need to pull the Docker image from the registry (e.g., Docker Hub). Use the following command to pull the `daphnejanelyn123/metagenomics-workshop` image: -docker pull daphnejanelyn123/metagenomics-workshop +docker pull ghcr.io/bioinfodlsu/metagenomics-workshop/deploy:latest This command fetches the image and prepares it for running in a container. @@ -43,8 +43,8 @@ This command fetches the image and prepares it for running in a container. You’ll want to mount your local directories to the Docker container to ensure that your notebooks, data, and results are accessible inside the container. Here’s a breakdown of the directories being mounted: -- **Data**: Your local path `path_to_your_data_directory (e.g., C:/Users/Daphne Go/.docker/bioinformatics/data)` containing the data will be mounted to `/home/jovyan/data` in the container. The data should be downloaded from the data folder located in this Drive Link (https://drive.google.com/drive/folders/1pfcwepIvSYmJ_wBp668jbVYR8nekrSF3?usp=sharing). Ensure that the required data files are placed in this directory before running the container. -- **Notebooks**: Your local path `path_to_your_notebooks_directory (e.g., C:/Users/Daphne Go/.docker/bioinformatics/notebooks)` will be mounted to `/home/jovyan/notebooks` in the container. The notebooks should be downloaded from the **notebooks folder in the Github repository provided**. Place your Jupyter notebooks into this local directory before running the container. +- **Data**: Your local path `path_to_your_data_directory` containing the data will be mounted to `/home/jovyan/data` in the container. The data should be downloaded from the data folder located in this Drive Link (https://drive.google.com/drive/folders/1pfcwepIvSYmJ_wBp668jbVYR8nekrSF3?usp=sharing). Ensure that the required data files are placed in this directory before running the container. +- **Notebooks**: Your local path `path_to_your_notebooks_directory` will be mounted to `/home/jovyan/notebooks` in the container. The notebooks should be downloaded from the **notebooks folder in the Github repository provided**. Place your Jupyter notebooks into this local directory before running the container. Make sure your data and notebooks are placed in your specified local directories before running the container. @@ -52,7 +52,7 @@ Make sure your data and notebooks are placed in your specified local directories Once the image is pulled and your directories are set up, run the Docker container with the following command: ``` -docker run -u root -e NB_USER="root" -e NB_UID=0 -e NB_GID=0 -e NOTEBOOK_ARGS="--allow-root" -p 8888:8888 -v "path_to_your_data_directory:/home/jovyan/data" -v "path_to_your_notebooks_directory:/home/jovyan/notebooks" daphnejanelyn123/metagenomics-workshop: metagenomics-workshop +docker run -u root -e NB_USER="root" -e NB_UID=0 -e NB_GID=0 -e NOTEBOOK_ARGS="--allow-root" -p 8888:8888 -v "path_to_your_data_directory:/home/jovyan/data" -v "path_to_your_notebooks_directory:/home/jovyan/notebooks" ghcr.io/bioinfodlsu/metagenomics-workshop/deploy:latest ``` Note: Please remember to replace the paths with your corresponding data and notebook directories. From aebe725cb2b5d12a3ee947f4c34b915bcdebf46b Mon Sep 17 00:00:00 2001 From: Daphne Go <77186592+daphnejanelyn@users.noreply.github.com> Date: Tue, 7 Jan 2025 09:57:25 +0800 Subject: [PATCH 2/2] Update README.md --- README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index e30420a..702eac7 100644 --- a/README.md +++ b/README.md @@ -32,9 +32,9 @@ This guide outlines the steps to **pull** a Docker image, mount necessary direct Note: Make sure you are running Docker Desktop or started your docker engine before performing any of the commands below. ### Step 1: Pull the Docker Image -First, you need to pull the Docker image from the registry (e.g., Docker Hub). Use the following command to pull the `daphnejanelyn123/metagenomics-workshop` image: +First, you need to pull the Docker image from the registry (e.g., Docker Hub). Use the following command to pull the image: -docker pull ghcr.io/bioinfodlsu/metagenomics-workshop/deploy:latest +`docker pull ghcr.io/bioinfodlsu/metagenomics-workshop/deploy:latest` This command fetches the image and prepares it for running in a container.