This repository hosts the code to deploy a webserver to wrap around the function of TB-Profiler. Updates will follow soon!
Installation requires tb-profiler, flask, celery and redis. To run it on your local machine:
# Install libraries
conda install python=3.7 flask redis celery statsmodels bwa samtools=1.10 bcftools=1.10 parallel freebayes>=1.3.5 gatk4 bedtools samclip delly=0.8.7 snpEff plotly weasyprint
pip install neo4j redis tqdm requests flask_sqlalchemy flask_login flask_session flask_wtf email_validator
python setup.py install
# Run flask
export FLASK_APP=tbdr
export FLASK_ENV=development
flask run
# Run rabbit-mq server
rabbitmq-server
# Run celery
celery -A tbdr.worker worker --loglevel=info --concurrency=1