1. Software Installation

Option 1 (highly recommended): use `apptainer`/`singularity`

We provide a pre-built Docker image on DockerHub for immediate usage.

Using KaMRaT within apptainer/singularity is highly recommended for users at any level unless the task involves in software development, because:

Building the container is simple and only requires the dependency of apptainer/singularity which should be pre-installed on most of HPC clusters.
Usage of KaMRaT in container ensures better reproducibility of results.
Several companion scripts can be easily run within the container, e.g., for input k-mer matrix construction.

In case when installation of apptainer is needed, please refer to their website for instructions.

To build apptainer/singularity image, please run:

apptainer build KaMRaT.sif docker://xuehl/kamrat:latest
    # alternatively to build singularity image: simply replace "apptainer" to "singularity"

CMake
MLPack >=4.0.0
Armadillo
Boost-iostreams
To use the provided Snakefile that builds input k-mer matrix from fastq files, Snakemake is also required

If you are installing MLPack with conda, please add the following line into your .bashrc file in the home/ directory before compiling KaMRaT:

export LD_LIBRARY_PATH=/path_to_conda_env/mlpack/lib:$LD_LIBRARY_PATH

git clone --recursive https://github.com/Transipedia/KaMRaT.git
cd KaMRaT
cmake . && make -j

Finally, an executable binary file is available as apps/kamrat.