5 stable releases
1.7.8 | Aug 24, 2024 |
---|---|
1.7.7 | Aug 23, 2024 |
1.7.6 | Aug 22, 2024 |
1.7.5 | Aug 19, 2024 |
1.7.4 | Aug 15, 2024 |
#130 in Biology
29 downloads per month
4MB
3.5K
SLoC
Uncerainty aware haplotype quantification using a Bayesian model that is based on collecting evidences from Varlociraptor.
Orthanq is under active development.
Installation
Orthanq is available as a Bioconda package and can be installed via:
mamba install orthanq
Haplotype quantification & HLA typing
Docs: https://orthanq.github.io/docs/index.html
Building for development and manual installation
The easiest way to build Orthanq is via Conda/Mamba.
First, create the environment given by the environment.yml
in this repository.
mamba env create -n orthanq-dev -f environment.yml
Second, activate the environment with
mamba activate orthanq-dev
Third, build Orthanq via
HDF5_DIR=$CONDA_PREFIX RUSTFLAGS='-L $CONDA_PREFIX/include' cargo build
Fourth, conda lib location is set via
export LD_LIBRARY_PATH=$CONDA_PREFIX/lib
Last, Orthanq can be built with:
cargo build
or
cargo build --release
Dependencies
~62MB
~1M SLoC