In this step, we add users to a Docker group in order to avoid prefacing docker commands with
sudo. This step needs to be performed once per individual Google Account using AutoLFADS or RADICaL, before they start a run.
First, navigate back to the compute engine and make sure the 'cloud shell' is open (button in the top right corner).
Again, this step only needs to be done ONCE per Google account. Thus, if prior to this your Google account has already been adding to the docker group, this step does not need to be repeated.
Furthermore, this step can only be done once the client machines are completely finished installing (remember to run check.sh to confirm this.)
Once the cloud shell is open, run the following command
sh add_docker_user.sh pbtclient.
For this tutorial, the command would be
sh add_docker_user.sh pbtclient
Leaving VMs running when not in use can lead to unintended high bills. Go to additional information section to see how to shut off unused VMs.
Adding user to docker group walkthrough
Next, we want to directly enter the server VM and copy the AutoLFADS or RADICaL code. In order to enter the server VM, we need to SSH in. First, make sure you're at the compute engine (console.cloud.google.com/compute) and can see your list of created VMs. Once you find your server you created (in this tutorial, its named tutserver), click on the button to the right of it labeled 'SSH'.
You have now SSHed into your server client. Now, inside this newly opened SSH browser window (NOT the cloud shell), we want to clone the repository here in order to obtain the AutoLFADS or RADICaL python script.
Run the following command in the SSH window.
For original AutoLFADS modeling spiking activity:
git clone -b GCP https://github.com/snel-repo/autolfads.git
For extensions of AutoLFADS modeling EMG and calcium (i.e., RADICaL) signals:
git clone -b GCP-extension https://github.com/snel-repo/autolfads.git
Now, the server VM should contain the necessary code.
This completes creating all the necessary cloud infrastructure.