Difference between revisions of "Team:USTC-Software/Installation"
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| − | sudo apt update | + | sudo apt update<br /> |
| − | sudo apt install git python3 python3-pip python3-biopython python3-flask python3-sqlalchemy python3-scipy libmysqlclient-dev mysql-server mysql-client wget | + | sudo apt install git python3 python3-pip python3-biopython python3-flask python3-sqlalchemy python3-scipy libmysqlclient-dev mysql-server mysql-client wget<br /> |
| − | git clone https://github.com/igemsoftware2016/USTC-Software-2016.git | + | git clone https://github.com/igemsoftware2016/USTC-Software-2016.git<br /> |
| − | cd USTC-Software-2016 | + | cd USTC-Software-2016<br /> |
| − | sudo pip3 install flask_login mysqlclient pymysql | + | sudo pip3 install flask_login mysqlclient pymysql<br /> |
| − | echo CREATE DATABASE biohub | mysql -u<user> -p # please fill in the blanks | + | echo CREATE DATABASE biohub | mysql -u<user> -p # please fill in the blanks<br /> |
| − | wget http://parts.igem.org/partsdb/download.cgi?type=parts_sql -O biobricks.sql.gz | + | wget http://parts.igem.org/partsdb/download.cgi?type=parts_sql -O biobricks.sql.gz<br /> |
| − | gunzip biobricks.sql.gz | + | gunzip biobricks.sql.gz<br /> |
| − | mysql -u<user> -p biohub < biobricks.sql # please fill in the blanks | + | mysql -u<user> -p biohub < biobricks.sql # please fill in the blanks<br /> |
| − | echo "DATABASE_URI = 'mysql://<username>:<password>@localhost/biohub'" >config.py # please fill in the blanks | + | echo "DATABASE_URI = 'mysql://<username>:<password>@localhost/biohub'" >config.py # please fill in the blanks<br /> |
| − | echo "SECRET_KEY = '<a random string>'" >>config.py # please fill in the blanks | + | echo "SECRET_KEY = '<a random string>'" >>config.py # please fill in the blanks<br /> |
| − | ./run.py | + | ./run.py<br /> |
| − | # then the server will start on port 5000 | + | # then the server will start on port 5000<br /> |
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Revision as of 23:07, 19 October 2016
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=
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
