Installation

ncbi-taxonomist is available on PyPi via pip. If you use another Python package manager than pip, please consult its documentation. If you are installing ncbi-taxonomist on a non-Linux system, consider the propsed methods as guidelines and adjust as required.

Important

Please note

If some of the proposed commands are unfamiliar to you, don’t just invoke them but look them up, e.g. in man pages or search online. Should you be unfamiliar with pip, check pip -h

Note

Python 3 vs. Python 2

Due to co-existing Python 2 and Python 3, some installation commands may be invoked slighty different. In addition, development and support for Python 2 did stop January 2020 and should not be used anymore.

ncbi-taxonomist requires Python >= 3.8. Depending on your OS and/or distribution, the default pip command can install either Python 2 or Python 3 packages. Make sure you use pip for Python 3, e.g. pip3 on Ubuntu.

Local pip install (no root required)

$: pip install ncbi-taxonomist --user

On Linux, ncbi-taxonomist will be installed to $HOME/.local/bin. If you cannot invoke ncbi-taxonomist from the command line, its’ likely $HOME/.local/bin is not in your $PATH (check echo $PATH). In such a case, choose one of the following possibilities:

• add $HOME/.local/bin to your $PATH:

  • echo "export PATH=${PATH}:$HOME/.local/bin" >> ~/.bashrc

• add an alias:

  • see man bash or https://www.tldp.org/LDP/abs/html/aliases.html

• use $HOME/.local/bin/ncbi-taxonomist implicitly

Global pip install (root required)

$: pip install ncbi-taxonomist

ncbi-taxonomist should be now in /usr/local/bin and in you $PATH.