Go Shell
Clone or download
Latest commit 9b540b5 Jul 9, 2018
Permalink
Failed to load latest commit information.
.github
doc
taxonkit
.gitignore
LICENSE
README.md
dev-version.md

README.md

TaxonKit - Cross-platform and Efficient NCBI Taxonomy Toolkit

Subcommands

  • list list taxon tree of given taxids
  • lineage query lineage of given taxids (supporting STDIN)
  • reformat reformat lineage (supporting STDIN)
  • name2taxid query taxid by taxon scientific name (supporting STDIN)

Misc

  • version print version information and check for update
  • genautocomplete generate shell autocompletion script

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