SynBioHub Docker Setups

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. Open terminal
2. git clone https://github.com/synbiohub/synbiohub-docker
3. docker-compose -f ./synbiohub-docker/docker-compose.yml up

With Explorer

To add SBOLExplorer, add the docker-compose.explorer.yml to the main docker-compose, i.e. for step 3 run docker-compose -f ./synbiohub-docker/docker-compose.yml -f ./synbiohub-docker/docker-compose.explorer.yml up

With sbol-db instead of Virtuoso

To run SynBioHub on sbol-db instead of Virtuoso, use docker-compose.sboldb.yml in place of the base docker-compose.yml:

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

This stack replaces the Virtuoso service with sbol-db (backed by Postgres). sbol-db answers on the virtuoso network alias at port 8890 and exposes the same HTTP SPARQL endpoints, so SynBioHub's triplestore configuration is unchanged — the triplestore is selected purely by which compose file you use. It requires a SynBioHub image with standards-compliant SPARQL (the triplestore-agnostic query fixes), which the published snapshot-standalone image carries.

With Plugins

To add plugins to the configuration change step 3 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

With Developmental SynBioHub

The docker-compose.version.yml can be added to another configuration, and simply contains the latest version of the SynBioHub docker image. This version does not even contain the Virtuoso image, so it should only be used by someone who knows what they are doing.

Plugins

For full plugin information please see this table which contains a sortable table with plugin overview.

Plugin Ports Used

Note that thee are other ports that are already in use: synbiohub:7777, virtuoso:8890, elasitcsearch:9200, sbolexplorer:13162, and xperimental-data-converter:3200.

• docker-compose.pluginVisualIgem.yml : 3000
• docker-compose.pluginVisualTest.yml : 8081
• docker-compose.pluginVisualTestJs.yml : 8082
• docker-compose.pluginDownloadSnapgene.yml : 8083
• docker-compose.pluginSubmitSnapgene.yml : 8084
• docker-compose.pluginVisualSeqviz.yml : 8085
• docker-compose.pluginVisualServeJs.yml : 8086
• docker-compose.pluginSubmitTest.yml : 8087
• docker-compose.pluginVisualServe.yml : 8088
• docker-compose.pluginDownloadTest.yml : 8089
• docker-compose.pluginDownloadTestJs.yml : 8090
• docker-compose.pluginSubmitTestJs.yml : 8091
• docker-compose.pluginDownloadTestEval.yml: 8092
• docker-compose.pluginSubmitExcelLibrary.yml: 8093
• docker-compose.pluginSubmitExcelComposition.yml: 8094
• docker-compose.pluginVisualComponentUse.yml : 8095
• docker-compose.pluginDownloadShortbol.yml : 8096
• docker-compose.pluginSubmitShortbol.yml : 8097
• docker-compose.pluginSubmitExcel2SBOL.yml : 8098
• docker-compose.pluginDownloadIbiosim.yml : 8099
• docker-compose.pluginDownloadSBOL2Excel.yml : 8100
• docker-compose.pluginAuthTest.yml : 8101
• docker-compose.pluginAuthFlapjack.yml : 8102
• docker-compose.pluginVisualFlapjack.yml : 8103
• docker-compose.AuthTesting.yml : 8104