Hackathon instructions

tutorials/hackathon_setup.md

@@ -1,7 +1,8 @@
 
 # 🐳 Minimal Jupyter via SSH + Docker (Lambda Cloud)
 
-This guide sets up Jupyter running **inside a Docker container** on your Lambda Cloud instance and forwards it securely to your local machine — without using Lambda's built-in JupyterLab.
+This guide sets up Jupyter running **inside a Docker container** on your 
+Lambda Cloud instance and forwards it securely to your local machine
 
 ---
 
@@ -19,6 +20,8 @@ Replace `<YOUR_SSH_KEY_PATH>` with your private key path and `<INSTANCE_IP>` wit
 
 ## ✅ 2. Start your Docker container with Jupyter
 
+Please replace the image URL with an image of your choosing. The BioNemo image has pytorch and datasets pre-installed 
+as well as implementations of several Bio-FMs.
 ```bash
 sudo docker run --gpus all --shm-size=64g -dit \
   --name bionemo \
@@ -37,11 +40,11 @@ sudo docker exec -it bionemo bash
 
 ## ✅ 3. Install Jupyter and other Python tools inside the container
 
-Inside the container shell:
+Inside the container shell, replace the pip and git commands with the packages that you need.
 
 ```bash
-pip install jupyter rapids-singlecell
-git clone -b tahoe-DGX-fix https://github.com/theislab/vevo_Tahoe_100m_analysis.git
+pip install jupyter anndata
+git clone https://huggingface.co/datasets/tahoebio/Tahoe-100M
 ```
 
 Then launch Jupyter:
@@ -57,6 +60,8 @@ Note the access token printed in the terminal output (you’ll need it to log in
 ## ✅ 4. Forward Jupyter port from remote to local
 
 On your **local machine**, open a new terminal and run:
+Please note that you can do the same port-forwarding setup to use VScode if you prefer.
+
 
 ```bash
 ssh -i <YOUR_SSH_KEY_PATH> -L 8888:127.0.0.1:8888 ubuntu@<INSTANCE_IP>
@@ -80,3 +85,4 @@ To stop and remove the container:
 sudo docker stop bionemo
 sudo docker rm bionemo
 ```
+