docker stop portainer-ce
docker rm portainer-ce
Those 2 commands will stop and remove the container respectively. Doing this will NOT remove your other applications/containers/etc.
Now that you have stopped and removed the old version of Portainer, you will want to ensure you have the latest version of the image locally. You can do this with a docker pull command:
docker pull portainer/portainer-ce
Finally, deploy the updated version of Portainer:
docker run -d -p 8000:8000 -p 9000:9000 --name=portainer-ce --restart=always -v /var/run/docker.sock:/var/run/docker.sock -v /docker-storage/portainer-ce:/data portainer/portainer-ce
The newest version of Portainer will now be deployed on your system, using the persistent data from the previous version, and will upgrade the Portainer database for the new version.
Install Portainer Agent
docker run -d -p 9001:9001 --name portainer_agent --restart=always -v /var/run/docker.sock:/var/run/docker.sock -v /var/lib/docker/volumes:/var/lib/docker/volumes portainer/agent