README.md

# PathoFact 1.0

PathoFact is an easy-to-use modular pipeline for the metagenomic analyses of toxins, virulence factors and antimicrobial resistance. 
Additionally, PathoFact combines the prediction of these pathogenic factors with the identification of mobile genetic elements. 
This provides further depth to the analysis by considering the localization of the genes on mobile genetic elements (MGEs), as well as on the chromosome. 
Furthermore, each module (toxins, virulence factors, and antimicrobial resistance) of PathoFact is also a standalone component, making it a flexible and versatile tool. 

# Requirements

PathoFact requires a good working Python (3.6.4), snakemake (version 5.5.4) and (mini)conda installation.
If snakemake is not yet installed one could install this by using the provided conda file (snakemake.yaml)
To install run: conda env create -f snakemake.yaml

PathoFact provides the conda environments with the dependencies needed to run the incorporated tools.
Some of the tools itself, however, still need to be installed. 
The following tools need to be installed by the user itself and the path to the tools adjusted within the config.yaml file:
  
    *HMMER-3.2.1
    *singalp-4.1

The following tools can either be installed manually or the set-up.sh script can be run to install automatically:

    *deepARG (v1)
    *PlasFlow (v1.1)
    *VirSorter (v1.0.5)
    *DeepVirFinder (v1.0)

It is recommended to install using the set-up.sh script. 
If installed manually make sure that the tools are installed in the folder "scripts" and the pathways matches those within the config.yaml
After the installation of deepARG make sure to manually adjust the configurations.

For this go to the directory where the program was saved (in this case the scripts/deeparg-ss directory within the PathoFact directroy) and open the files options.py.
Replace the path '/home/gustavo1/tmp/deeparg-ss/'; with the current directory (deepARG path).
Finally for LINUX system to allow diamond to be executed go to ./bin within the deeparg-ss directory and run:
chmod +x diamond
For more explanations on the deepArg configuration see the deepArg documentation: https://bitbucket.org/gusphdproj/deeparg-ss/src/master/