Difference between revisions of "Team:USTC-Software/Installation"
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We suggest users use Docker to deploy BioHub. It just needs two steps: | We suggest users use Docker to deploy BioHub. It just needs two steps: | ||
</p> | </p> | ||
| − | <p> | + | <p style="font-family:'Courier New' !important"> |
| − | + | docker run -d --name biohubdb -e MYSQL_ROOT_PASSWORD=password mysql | |
| − | + | <br /> | |
| − | + | docker run -d --name biohub --link biohubdb:db -p 80:5000 biohubtech/biohub | |
| − | + | ||
</p> | </p> | ||
<p> | <p> | ||
| − | You can also use < | + | You can also use <span style="font-family:'Courier New' !important">-e BIOHUB_DB_HOST=<host><span> and/or <span style="font-family:'Courier New' !important">-e BIOHUB_DB_USER=<user> -e BIOHUB_DB_PASSWORD=<password></span> to connect to other databases. |
</p> | </p> | ||
<p> | <p> | ||
Also, you can clone the repo and run it manually. We've tested this on Debian 8: | Also, you can clone the repo and run it manually. We've tested this on Debian 8: | ||
</p> | </p> | ||
| − | <p> | + | <p style="font-family:'Courier New' !important"> |
| − | + | 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 | |
| − | + | ||
| − | + | ||
</p> | </p> | ||
</div> | </div> | ||
Revision as of 23:05, 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
