ziemertlab/artswebapp repository overview

Note: This repository was last updated in 2017!

ARTS Web server: This is a sub repository for the Antibiotic Resistant Target Seeker. This can be used to view results generated from the public server at https://arts.ziemertlab.com⁠, or using output from the main analysis pipeline at https://bitbucket.org/ziemertlab/arts⁠

⁠I. Quickstart with Docker:

1- Install Docker and docker-compose: https://docs.docker.com/engine/installation/⁠ https://docs.docker.com/compose/install/⁠

2- Clone repository and change directory:

    git clone https://bitbucket.org/ziemertlab/artswebapp cd artswebapp

3- Edit docker-compose.yml to point to desired results directory:

    ##Example## ... volumes: -/my/path/to/results:/arts/results -/my/path/to/uploads:/arts/uploads ...

4- Build and run container: docker-compose up Notes:

• A pre-built image can also be run by downloading "docker-compose-artswebapp.yml" and running:

docker-compose -f docker-compose-artswebapp.yml up

• docker can run in the background using "-d" flag

docker-compose up -d

• list running docker images:

docker-compose ps

• Shutdown docker images

docker-compose down 

or

docker-compose -f docker-compose-artswebapp.yml down

• The full ARTS pipeline with analysis engine can be built using similar docker files at https://bitbucket.org/ziemertlab/arts⁠

⁠II. Installation on linux (Debian 8 tested):

1. Downlaod and install requirements::

    apt-get update
    apt-get install -y python-pip python-dev libjpeg-dev libfreetype6-dev zlib1g-dev
    git clone https://bitbucket.org/ziemertlab/artswebapp
    cd artswebapp
    pip install -r requirements.txt

1. Edit desired folders in configs (config/artsapp_default.conf and config/uwsgi.conf)
2. Run server (from arswebapp folder)::

    uwsgi --ini config/uwsgi.conf