Installation with Docker or Podman

This is the fastest way to get started with SmartScope.

Requirements

Warning

This has been tested with both Podman and Docker. In all the commands below, docker can be replaced by podman and docker-compose by podman-compose.

Docker

Docker is much easier to set up on most linux distributions and is therefore recommended.

Note

The latest versions of docker ship with docker-compose included. The commands shown below as docker-compose may have to be replaced with docker compose

Podman

Note

The installation requires Podman version >=3.0 and podman-compose 0.1.x. If you are using podman >=3.4, you can use podman-compose from the main branch on github.

Here are the links on how to install Podman and podman-compose:

Nvidia GPU passthrough (optional)

If you are planning on using GPU acceleration with SmartScope with podman, the nvidia-container-toolkit is required. The documentation on how to set it up for podman or docker can be found here

Installation steps

  1. Clone or download the git repository and navigate to the directory

    git clone https://github.com/NIEHS/SmartScope.git
cd SmartScope

  2. Using a text editor, copy the docker-compose-template.yml to docker-compose.yml and edit the values in the volumes and environment to your needs. The file includes description of each entry.

    Warning

    This is the most important step. Please follow the link below for a full description or the docker-compose file requirements.

    #Copy the template file
cp docker-compose-template.yml docker-compose.yml
#Open and edit with vim or other text editor
vim docker-compose.yml

  3. Run the docker-compose file. On the first run, this should build the images and start the pods.

    Note

    This process takes a few minutes to complete when the smartscope images needs to be built. You may be promtped to download images with multiple choices. Select the option that would pull from docker.io.

    #This will build and run the pod as a daemon
docker-compose up -d

    After the process is finished, you can list the running containers using the following command:

    docker ps
#Should produce the following output
CONTAINER ID  IMAGE                               COMMAND               CREATED       STATUS           PORTS                  NAMES
c4eaa0478684  k8s.gcr.io/pause:3.2                                      6 hours ago   Up 6 hours ago   0.0.0.0:48000->80/tcp  3e292605506f-infra
7bb77fe800e6  docker.io/library/mariadb:10.5      mysqld                6 hours ago   Up 6 hours ago   0.0.0.0:48000->80/tcp  smartscope-db
345730a43ad1  docker.io/library/redis:6.2-alpine  redis-server --sa...  6 hours ago   Up 6 hours ago   0.0.0.0:48000->80/tcp  smartscope-beta_cache_1
53310f8baf12  localhost/smartscope:0.62           gunicorn -c /opt/...  6 hours ago   Up 6 hours ago   0.0.0.0:48000->80/tcp  smartscope
ed4cf9175516  docker.io/library/nginx:latest      nginx -g daemon o...  6 hours ago   Up 6 hours ago   0.0.0.0:48000->80/tcp  smartscope-beta_nginx_1

    Note

    Anytime the docker-compose.yml is changed, the pod needs to be stopped and restarted. Stop with docker-compose down and start docker-compose up -d

    Altenatively, it is possible to build separately. To rebuild, add the –no-cache argument to the following command:

    #This will only the image building
docker-compose build
#To force rebuilding an existing image
docker-compose build --no-cache

  4. Log in to the web interface with the initial admin account.

    You should now be able to access the smartscope interface at http://localhost:48000/.

    The initial account is admin with password smartscope.

    Note

    You may need to change the domain and port number to reflect the docker-compose file with the port specified in the nginx service and one of the domains specified in the ALLOWED_HOSTS of the smartscope service.

  5. The installation is done!

    There is a few more set up steps to do in SerialEM and in the web portal to get up and running. Click here. for the instructions