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:
- 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.
-
Open the terminal/cmd in MacOS/Linux. For Windows OS make sure you open the command terminal as an administrator.
-
Navigate to the directory where you want to install SynBioHub.
For Mac/Linux/Windows OS use the following command to navigate:
cd directory_name
-
Subsequently, enter the following command into your terminal:
git clone https://github.com/synbiohub/synbiohub-docker
-
Then, enter the following command to start the local instance of SynBioHub:
docker-compose -f ./synbiohub-docker/docker-compose.yml up
-
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]
-
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.