TaxonKit - Cross-platform and Efficient NCBI Taxonomy Toolkit

Subcommands

Misc

Installation

Go to Download Page for more download options and changelogs.

TaxonKit is implemented in Go programming language, executable binary files for most popular operating systems are freely available in release page.

Method 1: Download binaries

Just download compressed executable file of your operating system, and decompress it with tar -zxvf *.tar.gz command or other tools. And then:

  1. For Linux-like systems

    1. If you have root privilege simply copy it to /usr/local/bin:

      sudo cp taxonkit /usr/local/bin/
      
    2. Or add the current directory of the executable file to environment variable PATH:

      echo export PATH=\$PATH:\"$(pwd)\" >> ~/.bashrc
      source ~/.bashrc
      
  2. For windows, just copy taxonkit.exe to C:\WINDOWS\system32.

Method 2: Install via conda Install-with-conda Anaconda Cloud downloads

conda install -c bioconda taxonkit

Method 3: For Go developer

go get -u github.com/shenwei356/taxonkit/taxonkit

Bash-completion

Note: The current version supports Bash only. This should work for *nix systems with Bash installed.

Howto:

  1. run: taxonkit genautocomplete

  2. create and edit ~/.bash_completion file if you don't have it.

    nano ~/.bash_completion
    

    add the following:

    for bcfile in ~/.bash_completion.d/* ; do
      . $bcfile
    done
    

Contact

Email me for any problem when using taxonkit. shenwei356(at)gmail.com

Create an issue to report bugs, propose new functions or ask for help.

License

MIT License