Installation

General

The docker-compose files in this repository represent various configurations for deploying SynBioHub. The files can be layered with Docker Compose’s multiple file capabilities.

The base configuration, described with docker-compose.yml, is simply SynBioHub, its graph database Virtuoso, and an autohealer.

To run the base configuration:

  1. Before trying to run SynBioHub locally on your PC, Make sure that you’ve Git and Docker installed.
  • Git:-

    For MacOS, click here.

    For Windows OS, click here

    For Linux/Unix OS, click here.

  • Docker:-

    For MacOS, click here.

    For Windows OS, click here. After installation make sure to run docker desktop as an administrator before moving to step two.

    For Linux OS, click here.

  1. Open the terminal/cmd in MacOS/Linux. For Windows OS make sure you open the command terminal as an administrator.

  2. Navigate to the directory where you want to install SynBioHub.

    For Mac/Linux/Windows OS use the following command to navigate:

    cd directory_name

  3. Subsequently, enter the following command into your terminal:

    git clone https://github.com/synbiohub/synbiohub-docker

  4. Then, enter the following command to start the local instance of SynBioHub:

    docker-compose -f ./synbiohub-docker/docker-compose.yml up

  5. In your browser search for localhost:7777 and it’ll take you to a setup page when you’ll run it for the very first time.

    [In case of Linux OS, if you face any permission errors, then simple insert sudo before every statement]

  6. The following command stops a local instance of SynBioHub:

    docker-compose -f ./synbiohub-docker/docker-compose.yml down

With SBOLExplorer

You can also run SynBioHub, by using SBOlExplorer. To add SBOLExplorer, add the docker-compose.explorer.yml to the main docker-compose, i.e. for step 5 run the following command:

sysctl -w vm.max_map_count=262144

docker-compose -f ./synbiohub-docker/docker-compose.yml -f ./synbiohub-docker/docker-compose.explorer.yml up

Presently, the command sysctl -w vm.max_map_count=262144 runs only on linux, due to OS upgrades on Mac OS*

With Plugins

To add plugins to the configuration, change the command mentioned in step 5 to:

docker-compose -f ./synbiohub-docker/docker-compose.yml -f ./synbiohub-docker/docker-compose.explorer.yml -f ./synbiohub-docker/docker-compose.<Plugin 1 File Name>.yml -f ./synbiohub-docker/docker-compose.<Plugin 2 File Name>.yml up

Note that all plugins are added before the up and each is preceeded by -f . For example, to run the configuration with the VisualIgem plugins and the VisualSeqviz plugin run:

docker-compose -f ./synbiohub-docker/docker-compose.yml -f ./synbiohub-docker/docker-compose.explorer.yml -f ./synbiohub-docker/docker-compose.pluginVisualIgem.yml -f ./synbiohub-docker/docker-compose.pluginVisualSeqviz.yml up

A table of currently available plugins can be found here.

Installation from source

Follow the instructions on the following GitHub README to install SynBioHub locally onto your system.