[DOC] Minor doc updates

docs/source/fedbiomed_node_part_2.md

@@ -9,7 +9,7 @@ scripts/vpn_status
 ```
 
 ```{code-block}
-:caption: Output
+:caption: Example output
 ** Checking docker containers & VPN access: vpn node
 - container vpn is running
 - container node is running

docs/source/index.md

@@ -17,6 +17,7 @@ includehidden:
 titlesonly:
 caption: Instructions
 ---
+prerequisites
 initial_setup
 freesurfer_idps
 phenotypic_files

docs/source/initial_setup.md

@@ -50,75 +50,6 @@ The above step installs three packages/tools:
 You can verify that they were installed successfully by running `<TOOL_NAME> --help`, where `<TOOL_NAME>` is one of `bagel`, `nipoppy`, and `brainflex`.
 This should print information about the CLI commands and options.
 
-## Check Docker and Docker Compose installations
-
-Make sure your Docker installation is working:
-
-```bash
-docker run hello-world
-```
-
-This command downloads a test image and runs it in a container.
-When the container runs, it prints a message like this before exiting:
-
-```{code-block}
-:caption: Output
-Hello from Docker!
-This message shows that your installation appears to be working correctly.
-
-To generate this message, Docker took the following steps:
- 1. The Docker client contacted the Docker daemon.
- 2. The Docker daemon pulled the "hello-world" image from the Docker Hub.
-    (amd64)
- 3. The Docker daemon created a new container from that image which runs the
-    executable that produces the output you are currently reading.
- 4. The Docker daemon streamed that output to the Docker client, which sent it
-    to your terminal.
-
-To try something more ambitious, you can run an Ubuntu container with:
- $ docker run -it ubuntu bash
-
-Share images, automate workflows, and more with a free Docker ID:
- https://hub.docker.com/
-
-For more examples and ideas, visit:
- https://docs.docker.com/get-started/
-```
-
-If Docker is not installed, see [these instructions](https://docs.docker.com/engine/install/) to install it and make sure to follow the [post-setup instructions](https://docs.docker.com/engine/install/linux-postinstall/).
-
-Also make sure Docker Compose is installed:
-
-```bash
-docker compose version
-```
-
-You should get something like this:
-
-```{code-block}
-Docker Compose version vX.Y.Z
-```
-
-```{attention}
-Installing Docker and Docker Compose requires `sudo` privileges.
-If you do not have `sudo` privileges, you will need to ask a system admin do to the installation for you.
-```
-
-### Troubleshooting
-
-If you get a `permission denied` error, check if your user is in the `docker` group:
-
-```bash
-groups
-```
-
-If `docker` is not in any of the groups listed, follow [this guide](https://docs.docker.com/engine/install/linux-postinstall/#add-your-user-to-the-docker-group) to add it.
-
-## Network prerequisite
-
-In order to join the federated network, the machine needs to have outbound UDP access to an external server (see `VPN_SERVER_ENDPOINT` in `config.env` file).
-Replies from the server must also be allowed back in.
-
 ## Node configuration
 
 ```{attention}

docs/source/prerequisites.md

@@ -0,0 +1,70 @@
+# Prerequisites
+
+## Docker and Docker Compose
+
+Make sure your Docker installation is working:
+
+```bash
+docker run hello-world
+```
+
+This command downloads a test image and runs it in a container.
+When the container runs, it prints a message like this before exiting:
+
+```{code-block}
+:caption: Output
+Hello from Docker!
+This message shows that your installation appears to be working correctly.
+
+To generate this message, Docker took the following steps:
+ 1. The Docker client contacted the Docker daemon.
+ 2. The Docker daemon pulled the "hello-world" image from the Docker Hub.
+    (amd64)
+ 3. The Docker daemon created a new container from that image which runs the
+    executable that produces the output you are currently reading.
+ 4. The Docker daemon streamed that output to the Docker client, which sent it
+    to your terminal.
+
+To try something more ambitious, you can run an Ubuntu container with:
+ $ docker run -it ubuntu bash
+
+Share images, automate workflows, and more with a free Docker ID:
+ https://hub.docker.com/
+
+For more examples and ideas, visit:
+ https://docs.docker.com/get-started/
+```
+
+If Docker is not installed, see [these instructions](https://docs.docker.com/engine/install/) to install it and make sure to follow the [post-setup instructions](https://docs.docker.com/engine/install/linux-postinstall/).
+
+Also make sure Docker Compose is installed:
+
+```bash
+docker compose version
+```
+
+You should get something like this:
+
+```{code-block}
+Docker Compose version vX.Y.Z
+```
+
+```{attention}
+Installing Docker and Docker Compose requires `sudo` privileges.
+If you do not have `sudo` privileges, you will need to ask a system admin do to the installation for you.
+```
+
+### Troubleshooting
+
+If you get a `permission denied` error, check if your user is in the `docker` group:
+
+```bash
+groups
+```
+
+If `docker` is not in any of the groups listed, follow [this guide](https://docs.docker.com/engine/install/linux-postinstall/#add-your-user-to-the-docker-group) to add it.
+
+## Network prerequisite
+
+In order to join the federated network, the machine needs to have outbound UDP access to an external server (see `VPN_SERVER_ENDPOINT` in `config.env` file).
+Replies from the server must also be allowed back in.