diff --git a/docs/source/fedbiomed_node_part_2.md b/docs/source/fedbiomed_node_part_2.md index 70ced2d..d38c0aa 100644 --- a/docs/source/fedbiomed_node_part_2.md +++ b/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 diff --git a/docs/source/index.md b/docs/source/index.md index 1547fa3..4eb2218 100644 --- a/docs/source/index.md +++ b/docs/source/index.md @@ -17,6 +17,7 @@ includehidden: titlesonly: caption: Instructions --- +prerequisites initial_setup freesurfer_idps phenotypic_files diff --git a/docs/source/initial_setup.md b/docs/source/initial_setup.md index d279b10..ede0bec 100644 --- a/docs/source/initial_setup.md +++ b/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 ` --help`, where `` 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} diff --git a/docs/source/prerequisites.md b/docs/source/prerequisites.md new file mode 100644 index 0000000..1ddd7ee --- /dev/null +++ b/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. diff --git a/src/brainflex/data/.env.example b/src/brainflex/data/.env.example deleted file mode 100644 index 6137a7b..0000000 --- a/src/brainflex/data/.env.example +++ /dev/null @@ -1,37 +0,0 @@ -# -# docker-compose.yml variables -# Copy to `.env` and edit as needed -# - -# Fed-BioMed version of the node image -# Must be the same version as the researcher and the VPN server -FBM_CONTAINER_VERSION_TAG=6.4.1 - -# Unique ID for this instance, among all the instances deployed on this machine -# (used in container names) -FBM_CONTAINER_INSTANCE_ID=default - -# Fed-BioMed node name, as shown to the researcher -#FBM_NODE_NAME= - -# Host user and group owning the files in `fbm-node` -# Set to the output of `id -u` and `id -g`. If unset, files are owned by UID/GID 2101 -#CONTAINER_UID= -#CONTAINER_GID= - -# Relative or absolute path to the Nipoppy study associated with this node -NIPOPPY_ROOT=./nipoppy_study - -# Researcher address on the VPN (Fed-BioMed VPN defaults) -#FBM_RESEARCHER_IP=10.222.0.2 -#FBM_RESEARCHER_PORT=50051 - -# Options passed to `fedbiomed node start`, eg `--gpu` -#FBM_NODE_START_OPTIONS= - -# Node security settings (Fed-BioMed defaults shown) -FBM_SECURITY_FORCE_SECURE_AGGREGATION=True -FBM_SECURITY_TRAINING_PLAN_APPROVAL=True -FBM_SECURITY_ALLOW_DEFAULT_TRAINING_PLANS=False -FBM_SECURITY_ALLOW_PREPROC=True -FBM_SECURITY_ALLOW_FEDERATED_ANALYTICS=True