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kmindex installation

Note

kmindex supports GNU/Linux systems, and macOS since v0.5.2.

Conda anaconda anaconda-platform

conda create -p kmindex_env
conda activate ./kmindex_env
conda install -c conda-forge -c tlemane kmindex

Note that the conda package includes kmtricks.

Docker dockerhub

docker pull tlemane/kmindex

Nix

  nix --extra-experimental-features 'nix-command flakes' build github:tlemane/kmindex

Release release

Portable binary releases are available at kmindex/releases.

Install from sources

Requirements

  • cmake >= 3.13
  • gcc >= 8.1
  • Boost.Asio and Boost.System >= 1.70
  • bzip2

All other dependencies are bundled with kmindex.

Installation 

git clone --recursive https://github.com/tlemane/kmindex # (1)!
cd kmindex && ./install.sh # (2)!

  1. Cloning the repository
  2. Build kmindex using install.sh

install.sh

kmindex build script - v0.5.0.
Usage:
  ./install.sh [-r str] [-t int] [-j int] [-p str] [-k int] [-n] [-h]
Options:
  -r <Release|Debug> -> build type {Release}.
  -t <0|1|2>         -> tests: 0 = disabled, 1 = compile, 2 = compile and run {0}.
  -j <INT>           -> nb threads {8}.
  -k <INT>           -> Max k-mer size (should be a multiple of 32) {256}
  -n                 -> portable x86-64 build {disabled}.
  -p                 -> install path {./kmindex_install}
  -h                 -> show help.