ubuntu.md

BioCompute Editor Setup: Ubuntu installation

For CentOS installation click here

1. install http server

sudo apt update

sudo apt install nginx

2. python3 and pip3, virtualenv install

sudo apt-get install build-essential libssl-dev libffi-dev python-dev

sudo apt install python3-pip

sudo pip3 install virtualenv

3. mongodb install

sudo apt update

sudo apt install -y mongodb

sudo systemctl status mongodb

4. Set up backend

Clone the project from git into home (or prefered) directory:

git clone https://github.com/ITsolution-git/bio-react.git

Example project directory for this manual:

/home/[user]/bio-react

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[user] should be replaced by current user name logged in centos

For example, assuming that current user name is centos: /home/centos/bio-react

---

/ you can skip this step to set virtual environment /

• set virtual environment in project directory:

virtualenv env

activate environment source env/bin/activate

sudo apt-get install postgresql

then fire:

sudo apt-get install python-psycopg2 and last:

sudo apt-get install libpq-dev`

• install packages in environment pip3 install -r requirements.txt

• migrate database: python3 manage.py migrate

• collect static: python3 manage.py collectstatic

• create admin: python3 manage.py createsuperuser

• You will be asked Admin Email, First/Last Name, and Password.

• allow domain/host:

Go to project root/django_react_proj, open settings.py. Then at line 27, you can see 'ALLOWED_HOSTS = []' You can add your domain or ip like this.

ALLOWED_HOSTS = ['biocomputeobject.org', '3.56.15.15']

There are allowed host names.

5. Set up frontend:

Copy the frontend project to /var/www sudo cp -rf ~/bio-react/frontend /var/www/

6. Deploy project

• install gunicorn sudo pip3 install gunicorn

• set gunicorn service to run django sudo vim /etc/systemd/system/gunicorn.socket

copy below content and insert to file open and save

[Unit]
Description=gunicorn socket

[Socket]
ListenStream=/var/www/gunicorn.sock

[Install]
WantedBy=sockets.target

Then: sudo vim /etc/systemd/system/gunicorn.service

[Unit]
Description=gunicorn daemon
Requires=gunicorn.socket
After=network.target

[Service]
User=[user]
Group=nginx
WorkingDirectory=/home/[user]/bio-react
ExecStart=/home/[user]/.local/bin/gunicorn \
          --access-logfile - \
          --workers 3 \
          --bind unix:/var/www/gunicorn.sock \
          django_react_proj.wsgi:application

[Install]
WantedBy=multi-user.target

---

[user] should be replaced by current user name logged in centos

---

• enable gunicorn socket: sudo systemctl enable gunicorn.socket

• enable and start gunicorn service:

  sudo systemctl enable gunicorn.service

  sudo systemctl start gunicorn.service

• check status gunicorn:

  sudo systemctl status gunicorn.service

You should get a notification that the service is working

• add to startup

  sudo systemctl daemon-reload

  sudo systemctl restart gunicorn

Make sure you replace SERVER_IP_OR_DOMAIN with your own server ip or domain address in the next steps

• Nginx Configuration

  sudo vim /etc/nginx/conf.d/biocompute.conf

server {
    listen 80;
    server_name 10.10.0.2;

    location = /favicon.ico { access_log off; log_not_found off; }

    # Django Admin assets
    location /assets/ {
        alias /home/centos/bco_editor/static/;
    }

    # Django Api access
    location /api/ {
        proxy_set_header Host $http_host;
        proxy_set_header X-Real-IP $remote_addr;
        proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
        proxy_set_header X-Forwarded-Proto $scheme;
        proxy_pass http://unix:/var/www/gunicorn.sock;
    }

    # Django Admin access
    location /admin {
        proxy_set_header Host $http_host;
        proxy_set_header X-Real-IP $remote_addr;
        proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
        proxy_set_header X-Forwarded-Proto $scheme;
        proxy_pass http://unix:/var/www/gunicorn.sock;
    }

    # Frontend access		    
    location / {
        autoindex on;
        root /var/www/frontend/build;
        index index.html;
        try_files $uri $uri/ =404;
    }
    error_page  404 /index.html;
    location = /index.html {
        root /var/www/frontend/build;
    }
	}

[user] should be replaced by the current user name logged in to centos

Test Nginx Configuration for syntax error: sudo nginx -t

Reload Nginx and restart this configuration: sudo systemctl restart nginx

If you use AWS, open a port number in Inbound Rule of AWS console.