Skip to content

Installation Methods

Please follow any of the options below to install ROADIES in your system.

  1. Install Conda (if not installed):
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
  1. Configure Conda channels:

conda config --add channels defaults

conda config --add channels bioconda

conda config --add channels conda-forge

Verify the installation by running conda in your terminal

  1. Create and activate a custom environment:

conda create -n roadies_env python=3.9 ete3 seaborn

conda activate roadies_env

  1. Install ROADIES:
conda install roadies=0.1.10
  1. Locate the installed files:
cd $CONDA_PREFIX/ROADIES

You will be able to find the contents of the repository within this ROADIES folder. Now you are ready to follow the Quick Start section to run the pipeline.

Option 2: Install via DockerHub

If you would like to install ROADIES using DockerHub, follow these steps:

  1. Pull the ROADIES image from DockerHub:

docker pull ang037/roadies:latest
2. Launch a container:

docker run -it ang037/roadies:latest

These commands will launch the Docker container in interactive mode, with the roadies_env environment activated and the working directory set to the ROADIES repository containing all necessary files. Once you are able to access the ROADIES repository, refer to the Quick Start section to run the pipeline.

Option 3: Install via Local Docker Build

  1. Clone the ROADIES repository:

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

cd ROADIES

  1. Build and run the Docker container:

docker build -t roadies_image .

docker run -it roadies_image

Once you are able to access the ROADIES repository, refer to Quick Start instructions to run the pipeline.

Option 4: Install via Source Script

  1. Install the following dependencies (requires sudo access):

  2. Java Runtime Environment (Version 1.7 or higher)

  3. Python (Version 3.9 or higher)
  4. wget and unzip commands
  5. GCC (Version 11.4 or higher)
  6. cmake (Download here: https://cmake.org/download/)
  7. Boost library (Download here: https://boostorg.jfrog.io/artifactory/main/release/1.82.0/source/)
  8. zlib (Download here: http://www.zlib.net/)

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
  1. Clone the repository:

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

cd ROADIES

  1. Run the installation script:

chmod +x roadies_env.sh

source roadies_env.sh

After successful setup (Setup complete message), your environment roadies_env will be activated. Proceed to Quick Start.

Note

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