Antibiotic Resistant Target Seeker (ARTS) Overview
ARTS is a webserver and analysis pipeline for screening for known and putative antibiotic resistance markers in order to identify and prioritize their corresponding biosynthetic gene clusters. ARTS can be installed locally or you can use the free public webserver located at https://arts.ziemertlab.com
See https://bitbucket.org/ziemertlab/artswebapp for a guide on installing the webserver independantly.
ARTS uses a webserver to queue jobs to the analysis pipeline. Details on webserver usage can be found at: https://arts.ziemertlab.com/help Alternatively jobs can be run directly using the artspipeline1.py script (see -h for options). Example:
artspipeline1.py antismashOutput.final.gbk reference/actinobacteria/ -rd myresults/ -cpu 8 -opt kres,phyl
ARTS Analysis server local install
The analysis server uses a daemon, runjobs.py, which consumes jobs submitted though the web interface.
Quick start with docker and docker compose:
For details on setting up docker and docker-compose see https://docs.docker.com/compose/install/ This will install local instances of the analysis and web server on a unix/linux system. For a windows installation see https://docs.docker.com/docker-for-windows/ The end result should be an directory with the docker-compose and ".env" file (On windows renaming a file ".file." will produce ".file", or choose save as "." in notepad)
Make an isolated directory and download the docker-compose file to install the pre-built ARTS containers:
mkdir ARTSdocker && cd ARTSdocker wget -O docker-compose.yml https://bitbucket.org/ziemertlab/arts/raw/HEAD/docker-compose-arts.yml
Set environment variables for multiprocessing, port number to run webserver, and shared folders of host system (replace /tmp with desired path or use these as the default):
echo "ARTS_RESULTS=/tmp" > .env echo "ARTS_UPLOAD=/tmp" >> .env echo "ARTS_RUN=/tmp" >> .env echo "ARTS_CPU=1" >> .env echo "ARTS_WEBPORT=80" >> .env
Build and start the services (from the ARTSdocker directory):
Shutting down services and clear containers from disk storage:
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
Source install on Debian 8
The following assumes a python2.7 environment with the pip package manager installed. It is recommended to use a virtual environment using virtualenv: https://virtualenv.pypa.io/en/stable/installation/
The analysis server will start a local antiSMASH job if cluster annotation is not already provided as input. See https://bitbucket.org/antismash/antismash for installation instructions.
Install required libraries and applications (root / sudo required):
apt-get update apt-get install -y wget python python-dev python-pip liblzma-dev \ libxml2-dev libxslt-dev zlib1g-dev libxext-dev libjpeg-dev \ libfreetype6-dev default-jre-headless mafft git git clone https://bitbucket.org/ziemertlab/arts cd arts pip install -r requirements.txt
Install required binaries from dependencies.txt file. Or use pre-compiled linux64bit bins (root / sudo required):
tar -xzf linux64_bins.tar.gz -C /usr/local/bin/ && hash -r
Edit configuration file to define server to listen for job submissions, antismash location, and custom folder paths
Start the analysis daemon (see -h for options):
python runjobs.py -pid /tmp/runjobs.pid
If you have any issues please feel free to contact us at firstname.lastname@example.org
This software is licenced under the GPLv3. See LICENCE.txt for details.