ARTS Web Server Overview

This is a sub repository for the Antibiotic Resistant Target Seeker (ARTS).

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://github.com/ziemertlab/arts

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

Installation of ARTS Web Server

There are three options for installing ARTS Web Server:

• Using Docker Images
• Using Anaconda/Miniconda
• Manual Installation for Linux/Ubuntu

1- Using Docker Image:

• Firstly, if you don't have Docker, you should install the Docker engine on your computer. Please check out the latest version of Docker on the official website.

• Edit desired paths to run Docker Images:

I- Desired Result Directory: /my/path/to/result_folders:/results/
II- Desired Log Directory: /my/path/to/log_file:/run/

• Enter the required paths and run the command:

docker run -it -v /my/path/to/results_folders:/results/ -v /my/path/to/log_file:/run/ -p 5000:5000 --rm ziemertlab/artswebapp-beta:latest

• You can see the other details on Docker Hub

2- Using Anaconda/Miniconda:

We recommend Anaconda3/Miniconda3 (with python >=3.8) and it is necessery for the conda package manager.

• Clone/Download the repository (root / sudo required):

    git clone https://github.com/ziemertlab/artswebapp

• Enter the artswebapp folder:

    cd artswebapp

• Create a new environment and install all the packages using the environment.yml file with conda:

    conda env create -f environment.yml

• Activate artswebapp environment:

    conda activate artswebapp

• Edit desired folders in configs (config/artsapp_default.conf and config/uwsgi.conf) (See Confugiration for more):
• Run server (from artswebapp folder) (See Usage for more):

    uwsgi --ini config/uwsgi.conf

3- Manual Installation for Linux/Ubuntu:

Note: Python version 3.8 or higher is recommended.

• Clone/Download the repository (root / sudo required):

    git clone https://github.com/ziemertlab/artswebapp

• Enter the artswebapp folder:

    cd artswebapp

• Install required libraries and applications (root / sudo required):

    pip install -r requirements.txt

• Edit desired folders in configs (config/artsapp_default.conf and config/uwsgi.conf) (See Confugiration for more):
• Run server (from artswebapp folder) (See Usage for more):

    uwsgi --ini config/uwsgi.conf

Configuration of ARTS Web Server

• Edit desired folders in configs (config/artsapp_default.conf and config/uwsgi.conf) and write your working directories instead of "~PATH":

EXAMPLE:
config/artsapp_default.conf:
        ...
        UPLOAD_FOLDER = "~PATH/uploads"
        RESULTS_FOLDER = "~PATH/results"
        ARCHIVE_FOLDER = "~PATH/archive"
        ...
config/uwsgi.conf:
        ...
        logto = ~PATH/artswebapp.log
        stats = ~PATH/uwsgi.stats.sock
        touch-reload = ~PATH/uwsgi.reload
        pidfile = ~PATH/uwsgi.pid
        ...

Usage of ARTS Web Server

• Run server (from artswebapp folder):

    uwsgi --ini config/uwsgi.conf

Note: It may need to run "redis-server" on the terminal.

• Click your local server on your browser:

    http://127.0.0.1:5000/

Note: The link may differ according to your configuration.

• Click result page to view ARTS results:

    http://127.0.0.1:5000/results

• Enter the result file name and click "View Report":

Note: Make sure your result folders are in the specified results folder path of artswebapp.conf.

config/artsapp_default.conf:
        ...
        RESULTS_FOLDER = "~PATH/results"
        ...

• You can view your ARTS results now!

Optional:

If you do not have a ARTS result file yet, you can download the sample result from the link below (~55MB). After extracting the zip file, follow the relevant steps.

  wget https://arts.ziemertlab.com/archive/GCF_000015125.1.zip
  unzip ~PATH/GCF_000015125.1.zip -d ~PATH/results/GCF_000015125.1

Optional - Submission a job using local webserver:

To start the analaysis on local webserver, please see https://github.com/ziemertlab/arts and install ARTS.

• Edit desired folders in configs (config/artsapp_default.conf and config/uwsgi.conf) and write all your working directories instead of "~PATH"

• Then, run server (from artswebapp folder)::

    uwsgi --ini config/uwsgi.conf

Note: It may need to run "redis-server" on the terminal.

• To submit an input file, run "runjobs.py" on the terminal:

    cd arts
    python runjobs.py run -pid /tmp/runjobs.pid

• Local webserver is ready to analyse!!

Support

If you have any issues please feel free to contact us at arts-support@ziemertlab.com

Licence

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

Publication

If you found ARTS to be helpful, please cite us:

Mungan,M.D., Alanjary,M., Blin,K., Weber,T., Medema,M.H. and Ziemert,N. (2020) ARTS 2.0: feature updates and expansion of the Antibiotic Resistant Target Seeker for comparative genome mining. Nucleic Acids Res.,10.1093/nar/gkaa374

Alanjary,M., Kronmiller,B., Adamek,M., Blin,K., Weber,T., Huson,D., Philmus,B. and Ziemert,N. (2017) The Antibiotic Resistant Target Seeker (ARTS), an exploration engine for antibiotic cluster prioritization and novel drug target discovery. Nucleic Acids Res.,10.1093/nar/gkx360