Installation¶
Build Requirements¶
| Requirement | Minimum Version | Ubuntu / Debian |
|---|---|---|
| C++20 compiler (GCC or Clang) | GCC 10+ / Clang 12+ | sudo apt install build-essential |
| CMake | 3.16+ | sudo apt install cmake |
| Boost (serialization, program_options, filesystem, system, math, iostreams) | 1.48+ | sudo apt install libboost-all-dev |
| ZLIB | --- | sudo apt install zlib1g-dev |
| BZip2 | --- | sudo apt install libbz2-dev |
| Git | --- | sudo apt install git |
Automatically fetched dependencies
SeqAn 2.5.2, GoogleTest, and NLopt are fetched automatically at configure time via CMake FetchContent. If they are already installed on your system, CMake will find them with find_package() instead.
Building from Source¶
git clone https://github.com/berntpopp/ReSeq2.git
cd ReSeq2
cmake -S . -B build
cmake --build build -j$(nproc)
Run the test suite to verify the build:
The executable will be at build/bin/reseq2.
System-wide Installation¶
# Install to /usr/local (default)
cmake --install build
# Or install to a custom prefix
cmake --install build --prefix /your/custom/prefix
Optional: Python Plotting Tools¶
ReSeq2 ships optional Python utilities for plotting and read-name preparation. To build the Python bindings, you need additional dependencies:
| Requirement | Minimum Version | Ubuntu / Debian |
|---|---|---|
| Python | 3.9+ | (usually pre-installed) |
| python3-dev | --- | sudo apt install python3-dev |
| SWIG | 3+ | sudo apt install swig |
Enable Python bindings at configure time:
Install the Python package:
This provides the reseq-prepare-names tool used for tile-aware mapping.
Bioconda¶
Bioconda package status
The current Bioconda reseq package installs the unmaintained upstream version. A dedicated reseq2 Bioconda package is planned for a future release. In the meantime, build from source for the latest features and fixes.
If you still want to install the legacy upstream version via Conda: