goetia is a c++ library and software package for streaming analysis for de Bruijn Graphs, de Bruijn graph compaction, and genome sketching. The c++ library is fully available through Python via bindings generated by cppyy. The primary goals of goetia and its algorithms are:
- Analyse data completely on-line with streaming methods,
- Use as little of the data as possible.
The primary supported platform is through conda. Within a conda environment, install with:
conda install goetia
This will install the goetia python package, install the libgoetia shared library
and its headers into $CONDA_PREFIX.
To build and install from source, first clone the repo:
git clone https://github.com/camillescott/goetia && cd goetia
Then create a conda environment:
conda create -y -n goetia -c conda-forge python=3 cppyy cmake cxx-compiler c-compiler clangdev libcxx libstdcxx-ng libgcc-ng pytest numpy scipy openmp python-clang screed blessings pytest-benchmark pyfiglet py-cpuinfo sourmash curio conda activate goetia
Then build and install with cmake:
mkdir build; cd build cmake .. make # optionally use -j N for faster/parallel build make install