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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

  1. 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.