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Developer Quickstart

Dependencies

Pre-commit

The project uses pre-commit to ensure code is consistently formatted; you can set this up using pip:

$ pip install pre-commit
$ pre-commit install

Linux dependencies

The following packages are necessary to build Dorado in a barebones environment (e.g. the official ubuntu:jammy Docker image).

$ apt-get update && apt-get install -y --no-install-recommends \
        curl \
        git \
        ca-certificates \
        build-essential \
        libhdf5-dev \
        libssl-dev \
        libzstd-dev \
        autoconf \
        automake
$ apt install gcc-9 g++-9 --no-install-recommends
$ update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-9 60 --slave /usr/bin/g++ g++ /usr/bin/g++-9

This project requires cmake 3.23 or higher. This can be installed via binary download from cmake.org or using python3-venv:

$ apt install python3-venv
$ python3 -m venv venv
$ . venv/bin/activate
$ pip install "cmake>=3.23"

Dorado requires CUDA 11.8 on Linux platforms. If the system you are running on does not have CUDA 11.8 installed, and you do not have sudo privileges, you can install locally from a run file as follows:

$ wget https://developer.download.nvidia.com/compute/cuda/11.8.0/local_installers/cuda_11.8.0_520.61.05_linux.run
$ sh cuda_11.8.0_520.61.05_linux.run --silent --toolkit --toolkitpath=${PWD}/cuda11.8

In this case, cmake should be invoked with CUDAToolkit_ROOT in order to tell the build process where to find CUDA:

$ cmake -DCUDAToolkit_ROOT=~/dorado_deps/cuda11.8 -S . -B cmake-build

Note that a suitable NVIDIA driver will be required in order to run Dorado.

All other dependencies will be fetched automatically by the cmake build process.

If libtorch is already downloaded on the host system and you do not wish the build process to re-download it, you can specify DORADO_LIBTORCH_DIR to cmake, in order to specify where the build process should locate it. For example:

$ cmake -DDORADO_LIBTORCH_DIR=/usr/local/libtorch -S . -B cmake-build

OSX dependencies

On OSX, version 2.69 of autoconf is required:

$ brew uninstall autoconf # not necessary if autoconf is not already installed
$ brew install autoconf@2.69
$ brew link autoconf@2.69

The following other packages need to be available as well

$ brew install openssl zstd

Clone and build

$ git clone https://github.com/nanoporetech/dorado.git dorado
$ cd dorado
$ cmake -S . -B cmake-build
$ cmake --build cmake-build --config Release -j
$ ctest --test-dir cmake-build

The -j flag will use all available threads to build Dorado and usage is around 1-2 GB per thread. If you are constrained by the amount of available memory on your system, you can lower the number of threads i.e. -j 4.

After building, you can run Dorado from the build directory ./cmake-build/bin/dorado or install it somewhere else on your system i.e. /opt (note: you will need the relevant permissions for the target installation directory).

$ cmake --install cmake-build --prefix /opt