Installation

How to install

fastCDS ships as a single package containing both a C++ binary (the index and map commands) and a Python wrapper (the fetch / plot commands, the Mapper API, and the DataFrame helpers). pip and bioconda both give you the whole thing.

pip

pip install fastCDS

The wheel bundles the compiled binary (as fastCDS/_bin/fastCDS-core), so all four commands work immediately - nothing else to install:

fastCDS --version
fastCDS fetch list

Ready-to-use wheels cover Linux and macOS (Intel + Apple Silicon), Python 3.9+. Windows is not supported directly - there's no Windows build, so run fastCDS inside WSL (Windows Subsystem for Linux), where it installs and behaves exactly like on Linux.

bioconda

conda install -c bioconda -c conda-forge fastCDS
# or, faster:
mamba install -c bioconda -c conda-forge fastCDS

conda compiles the binary as part of the recipe, so all four commands land on your PATH just like the pip install.

pixi

pixi resolves from the same conda channels:

pixi add -c bioconda -c conda-forge fastCDS      # in a project
pixi global install -c bioconda -c conda-forge fastCDS   # as a global tool

Build from source

Requirements:

• C++17 toolchain (g++ >= 9, clang >= 10, or MSVC >= 2019)
• CMake >= 3.16
• OpenMP (optional)

git clone https://github.com/SotoLF/fastCDS.git
cd fastCDS
mkdir build && cd build
cmake -DCMAKE_BUILD_TYPE=Release ..
make -j$(nproc)


pip install -e .

The repo's bin/fastCDS wrapper finds build/fastCDS automatically, so you can run the four commands straight from the checkout.

Docker

A Dockerfile at the repo root builds an image with the binary and wrapper ready to go:

docker build -t fastCDS .
docker run --rm -v "$(pwd):/work" fastCDS \
    map --index /work/human.idx --bed /work/queries.bed --out-dir /work/out --output all