Skip to content

Installation Methods

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

Note

The Bioconda install (Option 1) supports both Linux and macOS. GPU features (ROADIES_XP, optional) need Linux with an NVIDIA GPU and CUDA — there's no CUDA toolchain for macOS, so GPU-mode components aren't built there; CPU mode works on both. The source-script install (Option 4) is Linux-only (tested on Ubuntu 20.04/22.04).

  1. Install Conda, if you don't already have it:
wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
bash Miniconda3-latest-Linux-x86_64.sh
export PATH="$HOME/miniconda3/bin:$PATH" && source ~/.bashrc
  1. Create an environment and install ROADIES into it:
conda create -n roadies_env -c bioconda -c conda-forge roadies
conda activate roadies_env
  1. conda install puts the full repository contents (Snakemake rules, scripts, config.yaml, run_roadies.py, etc.) under $CONDA_PREFIX/ROADIES — that's your working directory from now on:
cd $CONDA_PREFIX/ROADIES

You're now ready for Quick Start — run it from this $CONDA_PREFIX/ROADIES directory (cd ROADIES if you've since moved elsewhere and need to get back).

Note

Bioconda's pasta package (the default multiple-sequence aligner) already installs run_pasta.py/run_seqtools.py correctly — no manual PASTA build should be needed. If the pipeline does fail on the PASTA step, see Troubleshooting: Issues with PASTA.

Option 2: Install via DockerHub

  1. Pull and run the prebuilt image:
docker pull ang037/roadies:latest
docker run -it ang037/roadies:latest

This launches an interactive container with the roadies_env conda environment already active and the working directory set to the ROADIES repository. Proceed to Quick Start.

Option 3: Install via Local Docker Build

  1. Clone the repository and build the image:
git clone https://github.com/TurakhiaLab/ROADIES.git
cd ROADIES
docker build -t roadies_image .
docker run -it roadies_image

Proceed to Quick Start once you're inside the container.

Option 4: Install via Source Script

  1. Install the system dependencies (requires sudo access): Java Runtime Environment (1.7+), Python (3.9+), wget/unzip, GCC (11.4+), cmake, Boost, zlib. On Ubuntu:
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 and run the setup script:
git clone https://github.com/TurakhiaLab/ROADIES.git
cd ROADIES
source roadies_env.sh

roadies_env.sh creates and activates the roadies_env conda environment, then builds everything ROADIES needs from source — PASTA, and (for ROADIES_XP) TWILIGHT plus, best-effort, MLIPPER if CUDA and libpll are already present. A Setup complete message means you're ready for Quick Start.

Note

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

Note

No extra steps are needed to use --mode placement; GPU placement (--gpu) does require a CUDA-capable GPU. See the ROADIES_XP guide for details, and re-run roadies_env.sh (or bash MLIPPER/install/setup_host.sh) once CUDA/libpll are available if MLIPPER was skipped at first setup.