vscode

docs/index.md

@@ -29,6 +29,9 @@ How to launch, access and get started using a notebook server.
 [Using the terminal](notebook-servers/using-the-terminal.md)  
 How to use the terminal inside a notebook server, with an explanation of caveats.
 
+[Using VS Code](using-vscode.md)
+How to connect to your CLIMB Notebook using VS Code
+
 [Understanding storage](storage/index.md)  
 An explanation of the different storage options available and when to use what.
 

docs/notebook-servers/index.md

@@ -20,5 +20,8 @@ How to install software using Conda, in the context of a containerized environme
 [Using Nextflow](using-nextflow.md)  
 How to use Nextflow with CLIMB-BIG-DATA.
 
+[Using VS Code](using-vscode.md)
+How to connect to your CLIMB Notebook using VS Code
+
 [How to fix login error 403](403-forbidden-error.md)  
 An explanation of how to resolve login error 403 when accessing notebooks.

docs/notebook-servers/using-vscode.md

@@ -0,0 +1,74 @@
+# Editing with VS Code
+
+Visual Studio Code, or VS Code, is a very popular [IDE](https://aws.amazon.com/what-is/ide/). 
+In this tutorial we will see how to use VS code to connect to your CLIMB Jupyter Notebook
+
+<!-- prettier-ignore -->
+!!! Prerequisites
+    We will assume you are a **VS Code** user already and you can install extensions and that you have a **GitHub account**.
+    If you are not, you might be interested in [learning why](https://code.visualstudio.com/learn) it's so popular, and maybe [download](https://code.visualstudio.com/Download) it and give it ago.
+
+
+## Install "Tunnels"
+
+Inside your local VS Code, install the extension `Remote - Tunnels` by Microsoft.
+
+After you install it, go to your *Remotes* tab and login using your GitHub account (you should see a *Sign in using your GitHub account* item in the menu).
+
+See the image below to locate the "Remotes" tab.
+
+![VS Code screenshot](img/vscode-remotes.png){ width=600 }
+
+## Install VS Code in your CLIMB terminal
+
+First, you will need to download *VS Code* also in your CLIMB notebook. This step has only to be done the first time.
+
+```console
+# SETUP (this has to be done once)
+cd $HOME
+# Download VS Code (this has to be done once)
+wget -O code.tgz "https://code.visualstudio.com/sha/download?build=stable&os=cli-alpine-x64"
+# Expand the package (this has to be done once)
+tar xvfz code.tgz
+```
+
+Now, you can run a tunnel from your CLIMB terminal, with this command:
+
+```console
+~/code tunnel
+```
+
+This command will start an *interactive* configuration walk-through so keep an eye at the terminal and 
+answer the questions / follow the instructions.
+
+You will have to follow the instructions which will involve:
+
+1. Selecting GitHub as provider
+2. Following the provided link and pasting there the code that will appear on your CLIMB notebook
+3. Authorize the connection
+4. Return to your CLIMB notebook terminal, and give a name to the connection
+
+Here a typical example of the connection setup:
+
+```text
+*
+* Visual Studio Code Server
+*
+* By using the software, you agree to
+* the Visual Studio Code Server License Terms (https://aka.ms/vscode-server-license) and
+* the Microsoft Privacy Statement (https://privacy.microsoft.com/en-US/privacystatement).
+*
+✔ How would you like to log in to Visual Studio Code? 
+· Github Account
+
+To grant access to the server, please log into https://github.com/login/device and use code 420D-0000
+
+✔ What would you like to call this machine? · jupyter-telatin-2enf
+[2024-03-18 12:25:40] info Creating tunnel with the name: jupyter-telatin-2enf
+
+Open this link in your browser https://vscode.dev/tunnel/jupyter-telatin-2enxf
+```
+
+When you are done, you can either click on the link provided on your terminal, or refresh
+your tunnels list in your *local* VS Code, and as shown in the image above, you should see the
+`jupyter-groupname-id` (or custom name you gave)

mkdocs.yml

@@ -50,6 +50,7 @@ nav:
       - "Understanding storage": "storage/index.md"
       - "Installing software with Conda": "notebook-servers/installing-software-with-conda.md"
       - "Using Nextflow": "notebook-servers/using-nextflow.md"
+      - "Using VS Code": "notebook-servers/using-vscode.md"
       - "403 Forbidden Error": "notebook-servers/403-forbidden-error.md"
   - "Walkthroughs":
       - "Metagenomics": "walkthroughs/metagenomics-tutorial.md"