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 /tmp directory (you can change the location, but don’t forget to update the config.py file)

mkdir /tmp/annso_v1
mkdir /tmp/annso_v1/cache
mkdir /tmp/annso_v1/downloads
mkdir /tmp/annso_v1/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 /tmp/annso_v1;
        }
}

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.

Run Annso

just

cd <ANNSO_PATH>/annso
make app

Using Annso

Create an analysis

todo

Setup samples

todo

Create and apply filters

todo

Select variant and get result

todo