SBOLExplorer is a service that simplifies the process of analyzing and searching for parts within genetic design repositories.
git clone https://github.com/michael13162/SBOLExplorer.git
.sysctl -w vm.max_map_count=262144
on Linux, or docker-machine ssh
then sysctl -w vm.max_map_count=262144
if you are on Windows or MacOS.pip install -r requirements.txt
to install all the dependencies. Try pip3
instead of pip
if that doesn't work../start.sh
in the SBOLExplorer/flask directory.curl -X GET "localhost:13162/update"
. Depending on repository size, this can take a couple of minutes.
http://localhost:13162/
as the SBOLExplorer endpoint, check the Searching Using SBOLExplorer
checkbox, 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.
Create a virtual environment in the parent directory. You can use the example commands below to create a virtualenv called sbol-explorer-venv
.
OS | Command |
---|---|
Ubuntu | virtualenv sbol-explorer-venv |
Mac | pyvenv sbol-explorer-venv |
Activate this virtualenv using the command source sbol-explorer-venv/bin/activate
(note: for the remainder of this guide, it will be assumed that your virtualenv is named sbol-explorer-venv
) You should see (sbol-explorer-venv)
before your command prompt if you've correctly activated the virtualenv.
Navigate into the flask
directory. Run the command pip install -r requirements.txt
to install all of the necessary Python packages for SBOLExplorer. You should now be able to start SBOLExplorer by running the start.sh script using the ./start.sh
command.
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.