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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
  1. Locate the installed files:
cd $HOME/miniconda3/envs/roadies_env/ROADIES

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

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.