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I have installed Anaconda (x64 Linux) and I am running its Python 3.

When I type which python, I get

/home/hinckelbc/anaconda3/bin/python

Now to display the version, I type python -V, and I get

Python 3.6.4 :: Anaconda, Inc.

Which is normal, since I am running Python 3 from Anaconda

If I launch Spyder from the terminal by simply typing spyder, it will launch and I see that the Python interpreter is indeed the Python 3 from Anaconda, as shown below:

Python 3.6.4 |Anaconda, Inc.| (default, Jan 16 2018, 18:10:19)
Type "copyright", "credits" or "license" for more information.

IPython 6.2.1 -- An enhanced Interactive Python.

!which python
/home/hinckelbc/anaconda3/bin/python

! python -V
Python 3.6.4 :: Anaconda, Inc.

The Spyder running on my machine is the following:

hinckelbc@BCArg:~$ which spyder
/home/hinckelbc/anaconda3/bin/spyder

In order to avoid opening the terminal all the time and typing spyder, I have created the following spyder.desktop file ~/.local/share/applications/spyder.desktop, which looks like this:

[Desktop Entry]
Type=Application
Name=Spyder
Exec=/home/hinckelbc/anaconda3/bin/spyder
Icon=/home/hinckelbc/anaconda3/pkgs/spyder-3.2.6-py36_0/info/icon.png
Terminal=false

I then could find Spyder with the Super key, which was then added to by launcher, by dragging and dropping (Gnome 3, Ubuntu 17.10)

However, when I open Spyder by clicking on the icon, now on my favorites, I get:

Python 3.6.4 |Anaconda, Inc.| (default, Jan 16 2018, 18:10:19)
Type "copyright", "credits" or "license" for more information.

IPython 6.2.1 -- An enhanced Interactive Python.

! which python
/usr/bin/python

! python -V
Python 2.7.14

Which does not agree with the python interpreter I set manually on Spyder, as shown below:

Does anyone know how to solve this, i.e. to get Python 3 running on Spyder with the desktop icon I have created and added to my favourites?

Your environment is different.

The spyder terminal inherits the PATH variable from its parent, the Spyder process, who has different env:
- When launching spyder from PATH is the one of shell, which includes .../conda/bin because of your .bashrc / .zshrc
- When launching from .desktop, the env is the one with /etc/profile (and maybe .profile ?)

In short, one solution is to launch through your shell:

Exec='bash -c .../spyder'

...and make sure that you add conda/bin to your PATH in .bash_profile, or see [How to load .bashrc from “bash -c”][1].