Get Started

Prerequisites

BioQueue can store data on SQLite, which means users can set up BioQueue without an extra database software. However, to achieve a higher performance, we suggest users to install MySQL. For Windows users, download the MySQL Installer or Zipped binary from MySQL. For POSIX compatible systems (like Ubuntu) users, running the following command should be enough to install MySQL server:

sudo apt-get install mysql-server mysql-client
sudo apt-get install libmysqld-dev
mysql -u root -p
CREATE DATABASE BioQueue;
CREATE USER 'bioqueue'@'localhost' IDENTIFIED BY 'YOURPASSWORD';
GRANT ALL PRIVILEGES ON BioQueue . * TO 'bioqueue'@'localhost';

Please replace ‘YOURPASSWORD’ with your own password for the database!

Since BioQueue is written in Python 2.7, please make sure that you have installed Python and pip. The following instructions are for Ubuntu 14.04, but can be used as guidelines for other Linux flavors:

sudo apt-get install build-essential
sudo apt-get install python-dev
sudo apt-get install python-pip

Installation

First of all, clone the project from github (Or you can download BioQueue by open this link):

git clone https://github.com/liyao001/BioQueue.git
Or
wget https://github.com/liyao001/BioQueue/zipball/master

NOTE:Download archives rather than use git makes it more difficult to stay up-to-date with BioQueue code because there is no simple way to update the copy.

Then navigate to the project’s directory, and run the install.py script (All dependent python packages will be automatically installed):

cd BioQueue
python install.py

When running install.py, this script will ask you a few questions including:

  1. CPU cores: The amount of CPU to use. Default value: all cores on that machine.
  2. Memory (Gb): The amount of memory to use. Default value: all physical memory on that machine.
  3. Disk quota for each user(Gb, default value: all disk space on that machine).

If you decide to run BioQueue with MySQL, the script will ask a few more questions:

  1. Database host: If you install MySQL server on your own machine, enter localhost or 127.0.0.1.
  2. Database user: user name of the database. bioqueue by default.
  3. Database password: password of the database.
  4. Database name: Name of the data table.
  5. Database port: 3306 by default

Start the queue

Run bioqueuepy script in the BioQueue/worker folder:

python worker/bioqueue.py

For Linux/Unix users, BioQueue can run in the background by running bioqueue_daemon.py instead of bioqueue.py:

python worker/bioqueue_daemon.py start

Start web server

Run the following command to start the webserver:

python manage.py runserver 0.0.0.0:8000

This will start up the server on 0.0.0.0 and port 8000, so BioQueue can be accessed over the network. If you want access BioQueue only in local environment, remove 0.0.0.0:8000. If you want to use BioQueue in a production environment, we recommend you to use a proxy server instead of manage.py (see detail at FAQ).

Start FTP server

BioQueue provides a FTP server to make it more convenient to transfer files, to run this server:

python worker/ftpserver.py

This step is optional, if you run command above, the FTP server will listen 20001 port by default. For Linux/Unix users, BioQueue FTP service can run in background by run ftp_daemon.py instead of ftpserver.py:

python worker/ftp_daemon.py start

Useful informations

  1. To stop the queue, the webserver or the FTP server, just hit Ctrl-c in the terminal from which BioQueue is running. If you run the queue or FTP server in the background, hit:

    python worker/bioqueue_daemon.py stop
python worker/ftp_daemon.py stop

  2. To get a better performance, moving the webserver to Apache or nginx is a good idea.