This is the new version of RAPPAS, currently under development.
- Boost Libraries >=1.6
- CMake >= 3.10
- GCC compiler must support c++17
- zlib
- rapidjson
In debian, these can be installed with:
sudo apt install build-essential cmake libboost-dev libboost-serialization-dev libboost-filesystem-dev libboost-iostreams-dev libboost-program-options-dev zlib1g-dev rapidjson-dev libquadmath0
git clone --recursive https://github.com/phylo42/rappas2.git
cd rappas2
./build.sh
The functionality of constructing new databases of phylo k-mers has been moved to xpas, a standalone tool for phylo k-mer database construction, which is a submodule of this repository.
Instead of running commands
python rappas2.py build OPTIONS...
which were supported in earlier versions of RAPPAS2, run:
python xpas.py build OPTIONS...
python rappas2.py place -i DATABASE -s [nucl|amino] -o OUTPUT_DIR INPUT_FASTA
See python rappas2.py place --help for more information.