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Last pushed: 6 days ago
Short Description
GUI for bioboxes.
Full Description

Biobox Gui

branch build status

A web application for running biobox containers.

What it does

Provides a web interface to run and add biobox containers, and track the states of their tasks, and with basic user handling.


Make sure you have Mesos 0.26.1, Docker, jkrue/jobproxy (commit: dddb503), and Mesos Chronos installed and running.

# must be on a filesystem shared by the mesos slaves
> export BIOBOX_HOST_BASE=$HOME/.biobox  #maybe add this to your .bashrc, change to your liking
# in case the jobproxy server is NOT on the docker host machine
> export JOBPROXY_URL=<URL jobproxy> # e.g. http://ser.ver:9999/v1/jobproxy


> docker run -d \
    -v $BIOBOX_HOST_BASE/data:/opt/application/data \
    -v $BIOBOX_HOST_BASE/db:/opt/application/db \


> git clone
> cd biobox-gui
> python3 -m venv venv     #setting up a virtual environment to avoid possible conflicts.
> source venv/bin/activate #switch to virtual environment
> pip install -r requirements.txt
> ./
  • visit http://localhost:5000/bioboxgui in your favourite webbrowser.
    • if you're running the app through docker, change localhost to the IP address of the container.
  • put your *.fq.gz files into $BIOBOX_HOST_BASE/data/input/files
  • the output will be found in $BIOBOX_HOSTBASE/data/output/\<date\>\\<container\>_\<task\>_\<user\>_\<hash\>/
  • add a source (e.g.
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