Quick guide¶
- Deploye and use Annso in 5 minutes. In the below tutorial :
- <HOST> : is the server host, by example “www.annso.com”
- <PORT> ! is the port that will be use by the annso python application, by example 8080
- <ANNSO_PATH> : is the path on the server where is deployed the pirus python application, by example “/var/annso_v1”
Installation¶
The following tutorial will show you how to set up a quick development environment for the annso application on a linux server. You may need to install first
sudo apt install build-essential libssl-dev libffi-dev python3-dev virtualenv libpq-dev
Annso need a postgresql database (9.5+). As ususal, you can customise value, just don’t forget to update the config.py file accordingly
sudo apt install postgresql
psql -U postgres -c "CREATE USER annso WITH PASSWORD 'annso';"
psql -U postgres -c "DROP DATABASE IF EXISTS annso;"
psql -U postgres -c "CREATE DATABASE annso;"
psql -U postgres -c "GRANT ALL PRIVILEGES ON DATABASE annso to annso;"
Then clone the repository and install requirements
git clone https://github.com/REGOVAR/Annso.git
cd Annso
virtualenv -p /usr/bin/python3.5 venv
source venv/bin/activate
pip install -r requirements.txt
You will need to create following empty folder in the /var directory (you can change the location, but don’t forget to update the config.py file)
mkdir -p /var/regovar/annso
mkdir /var/regovar/annso/cache
mkdir /var/regovar/annso/downloads
mkdir /var/regovar/annso/files
Init database
psql -U annso -d annso -f <ANNSO_PATH>/annso/database/create_all.sql
psql -U annso -d annso -f <ANNSO_PATH>/annso/database/scripts/import_refgen.sql
Using NginX¶
Create the file into /etc/nginx/sites-available/annso with the following content
Replace <PORT> and <HOST> with the good value:
#
# Virtual Host configuration for pirus.absolumentg.fr
#
upstream aiohttp_annso
{
server 127.0.0.1:<PORT> fail_timeout=0;
}
server
{
listen 80;
listen [::]:80;
server_name <HOST>;
location / {
# Need for websockets
proxy_http_version 1.1;
proxy_set_header Upgrade $http_upgrade;
proxy_set_header Connection "upgrade";
proxy_set_header Host $http_host;
proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
proxy_redirect off;
proxy_buffering off;
proxy_pass http://aiohttp_annso;
}
location /static {
root /var/regovar/annso;
}
}
Enable this virtual host by creating a symbolic link
sudo ln -s /etc/nginx/sites-enable/annso /etc/nginx/sites-available/annso
sudo /etc/init.d/nginx restart
Don’t forget to modify the <ANNSO_PATH>/annso/config.py file according to your configuration.