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Installation Methods

Using ROADIES Bioconda package

To run ROADIES using Bioconda package, follow these steps:

Note: You need to have conda installed in your system. Also make sure you have updated version of glibc in your system (GLIBC >= 2.29).

To install and use conda in Ubuntu machine, execute the set of commands below:

wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
chmod +x Miniconda3-latest-Linux-x86_64.sh
./Miniconda3-latest-Linux-x86_64.sh

export PATH="$HOME/miniconda3/bin:$PATH"
source ~/.bashrc

conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge

After this, try running conda in your terminal to check if conda is properly installed. Once it is installed, follow the steps below:

  1. Create and activate custom conda environment with Python version 3.9
conda create -n myenv python=3.9
conda activate myenv
  1. Install ROADIES bioconda package
conda install roadies

All files of ROADIES along with dependencies will be found in <conda_install_path>/miniconda3/envs/new_env/ROADIES.

Using DockerHub

To run ROADIES using DockerHub, follow these steps:

  1. Pull the ROADIES Docker image from DockerHub:

docker pull ang037/roadies:latest
2. Run the Docker container:

docker run -it ang037/roadies:latest

Using Docker locally

First, clone the repository (requires git to be installed in the system):

git clone https://github.com/TurakhiaLab/ROADIES.git
cd ROADIES

Then build and run the Docker container:

docker build -t roadies_image .
docker run -it roadies_image

Using installation script (requires sudo access)

First clone the repository:

git clone https://github.com/TurakhiaLab/ROADIES.git
cd ROADIES

Then, execute the installation script:

chmod +x roadies_env.sh
source roadies_env.sh

This will install and build all tools and dependencies. Once the setup is complete, it will print Setup complete in the terminal and activate the roadies_env environment with all Conda packages installed.

Note

ROADIES is built on Snakemake (workflow parallelization tool). It also requires various tools (PASTA, LASTZ, RAxML-NG, MashTree, FastTree, ASTRAL-Pro2) to be installed before performing the analysis. To ease the process, instead of individually installing the tools, we provide roadies_env.sh script to automatically download all dependencies into the user system.

Required dependencies

To run this script, ensure the following dependencies are installed: - Java Runtime Environment (version 1.7 or higher) - Python (version 3 or higher) - wget and unzip commands - GCC (version 11.4 or higher) - cmake (Download here: https://cmake.org/download/) - Boost library (Download here: https://boostorg.jfrog.io/artifactory/main/release/1.82.0/source/) - zlib (Download here: http://www.zlib.net/) - GLIBC (Version 2.29 or higher)

For Ubuntu, you can install these dependencies with: 

sudo apt-get install -y wget unzip make g++ python3 python3-pip python3-setuptools git default-jre libgomp1 libboost-all-dev cmake

Warning

If you encounter issues with the Boost library, add its path to $CPLUS_LIBRARY_PATH and save it in ~/.bashrc.