BioQueue is a web-based queue engine designed preferentially to improve the efficiency and robustness of job execution in bioinformatics research by estimating the system resources required by a certain job. At the same time, BioQueue also aims to promote the accessibility and reproducibility of data analysis in biomedical research. Implemented by Python 2.7, BioQueue can work in both POSIX compatible systems (Linux, Solaris, OS X, etc.) and Windows.
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 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';
Note: The following instructions are for Ubuntu 14.04, but can be used as a guideline for other Linux flavors. Please replace 'YOURPASSWORD' with your own password for the database!
apt-get install python-dev apt-get install python-pip
First of all, you will need to 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
Then navigate to the project's directory, and run
install.py script (All dependent python packages will be automatically installed):
cd BioQueue python install.py
install.py, this script will ask you a few questions include:
If you decide to run BioQueue with MySQL, the script will ask a few more questions:
bioqueue.py script in the
For Linux/Unix users, BioQueue can run in background by run
bioqueue_daemon.py instead of
python worker/bioqueue_daemon.py start
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
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
python worker/ftp_daemon.py start
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 background, hit
python worker/bioqueue_daemon.py stop python worker/ftp_daemon.py stop