Installation

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SynBioHub is deployed using Docker. Docker is a platform that allows pre-configured applications to be deployed anywhere, allowing SynBioHub to be installed as a single image with no prerequisites other than Docker itself.

From Prebuilt Image

First, install Docker.

Ensure that the Docker daemon is running on your system before continuing. On Mac and Windows, a small whale icon in the system tray indicates Docker is running.

Starting a SynBioHub container

To download and install SynBioHub automatically, simply run the command given below:

docker run -v synbiohub:/mnt -p 7777:7777 --name synbiohub -d synbiohub/synbiohub:1.2.0

On an Ubuntu system, the configuration files and database will be created in /var/lib/docker/volumes/synbiohub/_data/.

The -p option in the above command exposes port 7777 from the SynBioHub container to 7777 on the host machine. Therefore, SynBioHub will now be available at http://localhost:7777. SynBioHub can be used immediately with any of the client libraries or the RESTful API.

It is possible to start and stop the service as follows:

docker start synbiohub
docker stop synbiohub

If you no longer require the container, it can be deleted in the following way:

docker rm -v synbiohub

Note that any data stored in $HOME/synbiohub will not be deleted; you will need to delete the directory manually if you need to. Therefore, the docker rm operation is extremely useful when upgrading to a new SynBioHub image version, since your database and configuration files remain intact.

Configuring

On first startup, you will be taken to the SynBioHub Setup Page, which enables basic setup of the site. After first setup, the Admin Portal will allow admin users to update their site configuration.

SendGrid email setup

In order to enable SynBioHub to send account-related emails, you need a SendGrid account and API key. Once you have created your account, you should click "Settings" in the left bar, then "API Keys". On the resulting page, click the "Create API Key" button in the upper-right corner, and give your new API key a name. You should see the key on the next page. Copy the key and paste it into the "SendGrid API Key" in the Mail page on the SynBioHub admin dashboard. Save the API key in SynBioHub and you are ready to begin sending email.

Updating

To update to the latest version of SynBioHub, first stop and remove the container:

docker stop synbiohub
docker rm synbiohub

Then pull the latest version:

docker pull synbiohub/synbiohub:1.3.0

Finally, run a new container with the latest image:

docker run -v synbiohub:/mnt -p 7777:7777 --name synbiohub -d synbiohub/synbiohub:1.3.0

From Source

Follow the instructions on the GitHub README to install SynBioHub locally on your system. If you would like SynBioHub to run as a service, you can enable Virtuoso using systemd or open a virtual terminal using tmux or GNU screen and run

sudo /usr/local/bin/virtuoso-t +configfile $YOUR_CONFIG_FILE


You should also run SynBioHub as a system service or using a virtual terminal and the command

npm start

If you are doing development work, you can start SynBioHub with the command

npm run-script dev

which will restart the application with any change to the JavaScript source.

Publishing Instance

Nginx is used for the reference instance. NGINX configuration instructions




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