An end-to-end GPU-powered workflow for scRNA-seq using RAPIDS
Let's first verify that you have a working GPU, git, and Docker. Open up Terminal, then copy and paste in the below commands:
nvidia-smi
git --version
docker --version
nvidia-smi will output information about your GPU. If it doesn't, your GPU is not properly configured.git --version will print something like git version 2.43.0. If you get an error saying that git is not installed, please reinstall it.docker --version will print something like Docker version 28.3.3, build 980b856. If you get an error saying that Docker is not installed, please reinstall it. If you see a permission denied error, add your user to the docker group by running sudo usermod -aG docker $USER && newgrp docker.Open up Terminal, then copy and paste in the below commands:
git clone https://github.com/NVIDIA/dgx-spark-playbooks
cd dgx-spark-playbooks/nvidia/single-cell/assets
bash ./setup/start_playbook.sh
start_playbook.sh will:
Please keep the Terminal window open while using the playbook.
You can access your JupyterLab server in two ways
http://127.0.0.1:8888 if running locally on the DGX Spark.http://<SPARK_IP>:8888 if using your DGX Spark headless over your network.Once in JupyterLab, you'll be greeted with a directory containing scRNA_analysis_preprocessing.ipynb, and the folders cuDF, cuML, cuGraph, and playbook.
scRNA_analysis_preprocessing.ipynbis the playbook notebook. You will want to open this by double clicking on the file.cuDF, cuML, cuGraph folders contain the standard RAPIDS library example notebooks to help you continue exploring.playbook contains the playbook files. The contents of this folder are read-only inside of a rootless Docker Container.If you want to install any of the playbook notebooks on your own system, check out the readmes within the folder that accompanies the notebook
Once in JupyterLab, there all you have to do is run the scRNA_analysis_preprocessing.ipynb. You'll get both these playbook notebooks as well as the standard RAPIDS library example notebooks to help you get going.
You can use Shift + Enter to manually run each cell at your own pace, or Run > Run All to run all the cells.
Once you're done with exploring the scRNA_analysis_preprocessing notebook, you can explore other RAPIDS notebooks by going into the folders, selecting other notebooks, and doing the same thing.
Since the docker container cannot privileged write back to the host system, you can use JupyterLab to download any files you may want to keep once the docker container is shut down.
Simply right click the file you want, in the browser, and click Download in the dropdown.
Once you have downloaded all your work, go back to the Terminal window where you started running the playbook.
In the Terminal window,
Ctrl + Cy and then hit Enter at the prompt or hit Ctrl + C againWARNING
This will delete ALL data that wasn't already downloaded from the Docker container. The browser window may still show cached files if it is still open.