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https://github.com/synbiodex/sbolexplorer


https://github.com/synbiodex/sbolexplorer

synthetic-biology

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README 

        
# SBOLExplorer



SBOLExplorer is a service that simplifies the process of analyzing and searching for parts within genetic design repositories.



# Installation

1. 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.

2. Clone this repository with `git clone https://github.com/michael13162/SBOLExplorer.git`.

3. 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.

    * **Important**: If you are running ElasticSearch in Docker, make sure to run `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.

4. Install the latest version of Python 3 (https://www.python.org/downloads/).

5. Go to the SBOLExplorer/flask directory and run `pip install -r requirements.txt` to install all the dependencies.  Try `pip3` instead of `pip` if that doesn't work.

6. Run SBOLExplorer using `./start.sh` in the SBOLExplorer/flask directory.

7. 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.

   * Note: If you want to manually rename your index name in Elasticsearch after the initial creation, make sure to change the "elasticsearch_index_name" field in the config file.

8. Optionally, edit the "autoUpdateIndex" and "updateTimeInDays" fields in the config file to update your index automatically.

9. In SynBioHub, go to the Admin->General page and specify `http://localhost:13162/` as the SBOLExplorer endpoint, check the `Searching Using SBOLExplorer` checkbox, and click `Save`.  Searches will now go through SBOLExplorer.



![alt text](https://raw.githubusercontent.com/michael13162/SBOLExplorer/master/visualization/network.png)



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.



# Setting up a virtual environment

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.



# Automatic build and deploy

On each commit to master, a new Docker image is built and pushed to [Docker Hub](https://hub.docker.com/r/michael13162/sbolexplorer). 

This is done by TravisCI.

The credentials used to push the image are stored in Travis.