ARTS Web server overview

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 For usage of the web server see https://arts.ziemertlab.com/help

Quickstart with Docker local installation

For details on setting up docker and docker-compose: https://docs.docker.com/compose/install/

1. Make an isolated directory and download the docker-compose file to install the pre-built ARTS containers:

   mkdir ARTSwebapp_docker && cd ARTSwebapp_docker
   wget -O docker-compose.yml https://bitbucket.org/ziemertlab/artswebapp/raw/HEAD/docker-compose-artswebapp.yml
   

2. Set environment variables for port number to run webserver and shared folders of host system (replace /tmp with desired path):

   echo "ARTS_RESULTS=/tmp > .env"
   echo "ARTS_UPLOAD=/tmp >> .env"
   echo "ARTS_RUN=/tmp >> .env"
   echo "ARTS_WEBPORT=80 >> .env"
   

3. Build and start the services (from the ARTSdocker directory):

   docker-compose up
   

4. Shutting down services and clear containers from disk storage:

   docker-compose down
   

Extra) Start services in the background, check for running services, and shutdown without removing containers from disk:

docker-compose up -d
docker ps -a
docker-compose stop

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

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
   

2. Edit desired folders in configs (config/artsapp_default.conf and config/uwsgi.conf)

3. Run server (from arswebapp folder):

   uwsgi --ini config/uwsgi.conf
   

Source install on RHEL6:

This guide will compile python2.7 without disturbing the system's python2.6. Skip to step 4 if python2.7 and pip are pre-installed.

1. Install prerequisites for building python2.7. If no package manager is present, ensure the host has these requirements (root / sudo required):

   yum groupinstall development
   yum install openssl-devel sqlite-devel zlib-devel git
   export PATH="/usr/bin/local:$PATH"
   

2. Download sources for python, setuptools, artswebapp, pip install script:

   curl -O https://www.python.org/ftp/python/2.7.6/Python-2.7.6.tgz
   curl -O https://pypi.python.org/packages/61/3c/8d680267eda244ad6391fb8b211bd39d8b527f3b66207976ef9f2f106230/setuptools-1.4.2.tar.gz
   curl -O https://bootstrap.pypa.io/get-pip.py
   git clone https://bitbucket.org/ziemertlab/artswebapp
   

3. Setup new python2.7 alongside python2.6. Install setuptools and pip (root / sudo required):

   tar -xzf Python-2.7.6.tgz
   tar -xzf setuptools-1.4.2.tar.gz
   cd Python-2.7.6
   ./configure --prefix=/usr/local
   make && make altinstall
   cd ../setuptools-1.4.2
   python2.7 setup.py install
   python2.7 ../get-pip.py
   cd ../artswebapp
   

4. Install arts requirements using pip:

   pip2.7 install -r requirements.txt
   

5) Edit config/artsapp_default.conf to direct to desired results and upload folders Default uwsgi configs can now be used to run the webserver at port :5000 using uwsgi from the artswebapp directory:

nano config/uwsgi.config

6. Run artswebapp As a non-root user:

   uwsgi --ini config/uwsgi.config
   

The following may need to be set before users can connect:

setsebool -P httpd_can_network_connect 1

Extra) Use nginx to proxy port 80 to 5000. As root:

yum install nginx
mv /etc/conf.d/default.conf /etc/conf.d/default.bkup
cp config/nginx_siteavailible.conf /etc/conf.d/default.conf
sudo service nginx restart

Support

If you have any issues please feel free to contact us at [email protected]

Licence

This software is licenced under the GPLv3. See LICENCE.txt for details.