SBOLExplorer is a service that simplifies the process of analyzing and searching for parts within genetic design repositories. For questions, contact Michael Zhang at firstname.lastname@example.org
- These installation steps assume you have the latest version of SynBioHub up and running on http://localhost:7777. For instructions, see https://github.com/SynBioHub/synbiohub.
- Clone this repository with
git clone https://github.com/michael13162/SBOLExplorer.git.
- Install and run ElasticSearch 6.3 (https://www.elastic.co/guide/en/elasticsearch/reference/current/install-elasticsearch.html).
- The exact steps will depend on your environment, so read the manual (aka RTFM).
- Set up the package repo to install ElasticSearch from.
- Install ElasticSearch.
- Start ElasticSearch (will be different depending on init vs systemd).
- Optionally, configure ElasticSearch to start on boot.
- Install the latest version of Python 3 (https://www.python.org/downloads/).
- Go to the SBOLExplorer/flask directory and run
pip install -r requirements.txtto install all the dependencies. Try
pipif that doesn't work.
- Run SBOLExplorer using
./start.shin the SBOLExplorer/flask directory.
- To update the index for the first time, run
curl -X GET "localhost:13162/update". Depending on repository size, this can take a couple of minutes.
- Optionally, run
crontab update.cronto automatically update SBOLExplorer periodically.
- To change the update period, edit update.cron
- In SynBioHub, go to the Admin->General page and specify
http://localhost:13162/as the SBOLExplorer endpoint, check the
Searching Using SBOLExplorercheckbox, and click
Save. Searches will now go through SBOLExplorer.
To run a neat visualization, go to the force_directed_graph folder and run "http-server" in the command line. Then, open the browser to the hosted page. Shown is a network visualization of part usage in SynBioHub.
Automatic build and deploy
On each commit to master, a new Docker image is built and pushed to Docker Hub. This is done by TravisCI. The credentials used to push the image are stored in Travis.