Team:USTC-Software - 2016.igem.org

Install BioHub

We suggest users use Docker to deploy BioHub. It just needs two steps:

									docker run -d --name biohubdb -e MYSQL_ROOT_PASSWORD=password mysql
									docker run -d --name biohub --link biohubdb:db -p 80:5000 biohubtech/biohub

You can also use

-e BIOHUB_DB_HOST=<host>

and/or

-e BIOHUB_DB_USER= -e BIOHUB_DB_PASSWORD=<password>

to connect to other databases.

Also, you can clone the repo and run it manually. We've tested this on Debian 8:

									sudo apt update
									sudo apt install git python3 python3-pip python3-biopython python3-flask python3-sqlalchemy python3-scipy libmysqlclient-dev mysql-server mysql-client wget
									git clone https://github.com/igemsoftware2016/USTC-Software-2016.git
									cd USTC-Software-2016
									sudo pip3 install flask_login mysqlclient pymysql
									echo CREATE DATABASE biohub | mysql -u<user> -p # please fill in the blanks
									wget http://parts.igem.org/partsdb/download.cgi?type=parts_sql -O biobricks.sql.gz
									gunzip biobricks.sql.gz
									mysql -u<user> -p biohub < biobricks.sql # please fill in the blanks
									echo "DATABASE_URI = 'mysql://<username>:<password>@localhost/biohub'" >config.py # please fill in the blanks
									echo "SECRET_KEY = '<a random string>'" >>config.py # please fill in the blanks
									./run.py
									# then the server will start on port 5000

Team:USTC-Software/Installation

Install BioHub