Installation

MGEfinder has only been tested on linux-64 and MacOSX systems. We currently support two methods of installation, described below. If you run into trouble, do not hesitate to report an issue.

Installation Method 1: Installing MGEfinder from conda environment file

This method of installation is currently the simplest, fastest, and most reliable.

1) Install Miniconda

Execute the following commands, and make sure to answer yes to all questions asked by the miniconda installer:

     wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
     bash Miniconda3-latest-Linux-x86_64.sh
     rm Miniconda3-latest-Linux-x86_64.sh
     source ~/.bashrc

2) Download and install MGEfinder

Execute the following commands to install MGEfinder on your machine:

     git clone https://github.com/bhattlab/MGEfinder.git
     cd MGEfinder/
     bash install.sh

3) Activate conda environment and install

First you'll want to activate the mgefinder conda environment. You'll need to repeat this step whenever use mgefinder.

     conda activate mgefinder

Now you should be able to use mgefinder. Test it by executing

     mgefinder --help

Try going through the tutorial to learn how to use mgefinder

Installation Method 2: MGEfinder Singularity Container

Singularity containers are like docker containers but they work better in high-performance computing (HPC) environments. A singularity container running MGEfinder can be downloaded directly and run as follows:

1) Install singularity

Singularity requires root privileges to run properly. If you are using an HPC cluster, ask your admin to install it. If you have root privileges yourself, you can download the latest release of singularity here.

2) Download MGEfinder singularity container

You can download the container from Singularity-Hub using the following command:

     singularity pull --name mgefinder.simg shub://bhattlab/MGEfinder-singularity

3) Run MGEfinder

You can then easily run MGEfinder with a command such as:

     singularity run mgefinder.simg mgefinder workflows test_workdir/

NEXT: Step-by-step tutorial