Webserver

LSHTM TB-Profiler webserver

If you don't have access to a linux or macOS environment you can still use tb-profiler by using our webserver http://tbdr.lshtm.ac.uk/

You can upload your next generation sequencing data in fastQ format. You can upload one or two (forward and reverse) fastq files. When you upload your data, the run will be be assigned a unique ID. Please take a note of this ID as you will need to to find your results later. Batch upload of samples is also possible.

Setting up your own webserver

The code for the webserver http://tbdr.lshtm.ac.uk/ is available on here. This is still in early development but you can use it to set up your own instance of the server. To do this run the following code

# Install libraries
git clone https://github.com/jodyphelan/tb-profiler-webserver.git
cd tb-profiler-webserver
python setup.py install

# Run flask
export FLASK_APP=tbprofiler_web
export FLASK_ENV=development
flask run

# Run rabbit-mq server
rabbitmq-server

# Run celery
celery -A tbprofiler_web.worker worker --loglevel=info --concurrency=1