Ok, so I am in my anaconda environment and I ran which python. I get


Now if I start tmux, then run source activate env1, then which python, I get


even though I do have my environment activated. How can I make anaconda see the same path inside tmux ?


The solution seems to be to deactivate the conda environment, then start tmux, then reactivate the environment inside tmux.

  • 2
    Weird solution but works ... – LYu Oct 16 '18 at 17:18
  • That's weird indeed. – ZirconCode Nov 14 '18 at 21:23
  • 1
    I'm upvoting because this is the solution that worked for me, however it is really a far from ideal solution – johnchase Feb 6 at 23:13


conda activate env1

Instead of:

source activate env1

When inside tmux worked for me.


The following happens to me after starting a Tmux session (without conda having any active env).

When I first do inside the Tmux session:

conda activate myEnv

I get

CommandNotFoundError: Your shell has not been properly configured to use 'conda activate'.
To initialize your shell, run

    $ conda init <SHELL_NAME>

Currently supported shells are:
  - bash
  - fish
  - tcsh
  - xonsh
  - zsh
  - powershell

See 'conda init --help' for more information and options.

IMPORTANT: You may need to close and restart your shell after running 'conda init'.

If instead I do:

source deactivate
conda activate myEnv

Everything works just fine. which python points to the correct path.


This behaviour is caused by TMux sourcing ~/.profile instead of ~/.bashrc. My ~/.profile is this:

# if running bash
if [ -n "$BASH_VERSION" ]; then
    # include .bashrc if it exists
    if [ -f "$HOME/.bashrc" ]; then
    . "$HOME/.bashrc"

# set PATH so it includes user's private bin if it exists
if [ -d "$HOME/bin" ] ; then

# set PATH so it includes user's private bin if it exists
if [ -d "$HOME/.local/bin" ] ; then

You can see that first ~/.bashrc is sourced and then ~/bin and ~/.local/bin are prepended. As I experienced myself, this causes conda to hickup.

The solution would be to comment out the two blocks manipulating PATH in ~/.profile.

nano ~/.bash_profile

Add the following lines:

source deactivate env1
source activate env1

worked for me.

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