Content
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.htmluse
$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
.