FunARTS Web Server Overview

This is a sub repository for the Fungal bioActive compound Resistant Target Seeker (FunARTS).

This can be used to view results generated from the public server at https://funarts.ziemertlab.com or using output from the main analysis pipeline at https://github.com/ziemertlab/funarts

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

Installation of FunARTS Web Server

There are three options for installing FunARTS 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:/result_folders/ -v /my/path/to/log_file:/run/ -p 5000:5000 ziemertlab/funartswebbapp:latest

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 (~15MB) (root / sudo required):

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

• Enter the funartswebapp folder:

    cd funartswebapp

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

    conda env create -f environment.yml

• Activate funartswebapp environment:

    conda activate funartswebapp

• Edit desired folders in configs (config/funartsapp_default.conf and config/uwsgi.conf) (See Confugiration for more):
• Run server (from funartswebapp 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 (~15MB) (root / sudo required):

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

• Enter the funartswebapp folder:

    cd funartswebapp

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

    pip install -r requirements.txt

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

    uwsgi --ini config/uwsgi.conf

Configuration of FunARTS Web Server

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

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

Usage of FunARTS Web Server

• Run server (from funartswebapp 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 FunARTS 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 funartswebapp.conf.

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

• You can view your FunARTS results now!

Optional:

If you do not have a FunARTS result file yet, you can download the sample result from the link below (~85MB). After extracting the zip file, follow the relevant steps.

  wget https://funarts.ziemertlab.com/archive/GCF_001890705.1.zip
  unzip ~PATH/GCF_001890705.1.zip -d ~PATH/results/GCF_001890705.1

Optional - Submission a job using local webserver:

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

• 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 funartswebapp 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 funarts
    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 FunARTS to be helpful, please cite us:

Yılmaz, T. M., Mungan, M. D., Berasategui, A., & Ziemert, N. (2023). FunARTS, the Fungal bioActive compound Resistant Target Seeker, an exploration engine for target-directed genome mining in fungi. Nucleic Acids Research