Merge pull request #11 from PDBeurope/PDBE-7052

Docker install option

.dockerignore

@@ -0,0 +1,38 @@
+
+
+# Common
+README.md
+CHANGELOG.md
+docker-compose.yml
+Dockerfile
+
+# Virtual environments
+venv
+env
+.venv
+.env
+
+# Python
+*.pyc
+.Python
+
+# Editors
+vscode
+.idea
+
+# Git
+.git
+.gitignore
+.gitattributes
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.coverage
+.cache
+nosetests.xml
+coverage.xml
+
+# Trash
+pdbe_tutorial_2024/.Trash-0/
+.Trash-0/

.gitignore

@@ -1,10 +1,22 @@
 .ipynb_checkpoints
 .idea
-venv
 *.pyc
 
 summer_school_2024/similar_proteins*
 summer_school_2024/search_results*
 
 pdbe_tutorial_2024/similar_proteins*
 pdbe_tutorial_2024/search_results*
+
+# Environments
+env/
+venv/
+.venv/
+.env/
+
+# Editors
+.vscode/
+
+# Trash
+pdbe_tutorial_2024/.Trash-0/
+.Trash-0/

Dockerfile

@@ -0,0 +1,15 @@
+FROM python:3.10
+
+LABEL maintainer="pdbegroup"
+
+WORKDIR /pdbe_api_tutorial
+
+COPY ./requirements.txt /pdbe_api_tutorial/requirements.txt 
+
+RUN pip install --no-cache-dir -r requirements.txt
+
+EXPOSE 8888
+
+COPY ./pdbe_tutorial_2024 /pdbe_api_tutorial/pdbe_tutorial_2024
+
+CMD ["jupyter-server", "--allow-root", "--ip", "0.0.0.0", "--port", "8888", "--no-browser", "pdbe_tutorial_2024/"]

LICENSE.md

@@ -1,4 +1,4 @@
-Copyright 2018 EMBL - European Bioinformatics Institute
+Copyright 2024 EMBL - European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.

README.md

@@ -2,41 +2,68 @@
 
 This repository contains Jupyter Notebooks that can be used as training materials for understanding how the PDBe REST API works, and provides a number of examples of answering specific questions about PDB entries using the API.
 
-## Getting Started
 
-Either use Binder to use the notebook:
+## Getting started with Docker (recommended)
 
-[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/PDBeurope/pdbe-api-training/master)
+This option launches the summer school notebooks in a Docker container. This is the recommended way to run the notebooks as it ensures that all dependencies are correctly installed and that the notebooks will run as expected.
 
-Or
+Make sure your [Docker](https://docs.docker.com/engine/install/) is running on your machine before executing the following commands:
 
-You will need to have Jupyter installed on your machine. For Linux/OSX machines, simply type:
+### Clone the repository
+```console
+git clone https://github.com/PDBeurope/pdbe-api-training .
+cd /path/to/your/pdbe-api-training/
+```
 
+### Build the Docker container (you only need to do this once)
+```console
+docker build -t pdbe-api-training .
 ```
-pip3 install --upgrade pip
-pip3 install jupyter
+
+### Run the Docker container
+```console
+docker run -p 8888:8888 -v /path/to/your/pdbe-api-training/pdbe_tutorial_2024/:/pdbe_api_tutorial/pdbe_tutorial_2024 pdbe-api-training
 ```
 
-For Windows machines (optionally also for Linux/OSX) you can install Jupyter with Anaconda:
-https://www.anaconda.com/download/
+Now open your browser and go to `http://localhost:8888/` and you should see the Jupyter Notebook interface. The `-v` flag ensures changes you make to the notebooks will be saved in the `pdbe_tutorial_2024` directory in the repository cloned to your local machine.
+
+## Getting started with Binder
 
-### Prerequisites
+Notebooks can also be run on cloud via Binder. Click on the badge below to launch the notebooks in Binder:
+
+[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/PDBeurope/pdbe-api-training/master)
 
-If installing using Anaconda, there is no additional prerequisites. If installing using pip3, you will need to have Python3 on your machine, and of course pip3
 
-### Installing
+## Getting started with Python and Jupyter
 
-From command line on Unix machine these would be the steps setting up everyone:
+You will need to have Python3.10, pip3 and Jupyter installed on your machine.
 
+### Upgrade pip3
+```console
+pip3 install --upgrade pip
 ```
+
+For Windows machines (optionally also for Linux/OSX) you can install Jupyter with conda-forge:
+https://conda-forge.org/
+
+### Clone the repository
+
+```console
 mkdir pdbe_jupyter
 cd pdbe_jupyter
 git clone https://github.com/PDBeurope/pdbe-api-training .
-jupyter notebook
+```
+
+### Install the dependencies and start Jupyter
+```console
+cd pdbe-api-training
+pip3 install -r requirements.txt
+jupyter ./pdbe_tutorial_2024
 ```
 
 Jupyter Notebook will open a window in your browser, and you can select the specific notebooks you would like to view.
 
+
 ## Authors
 
 * **Mihaly Varadi** - *Initial work* - [github](https://github.com/mvaradi)