run a crontab job using an anaconda env

After MUCH fiddling I got crontab to activate my conda environment with conda activate my_env and run the Python interpreter within that environment.

Note I'm using Ubuntu 18.04.

Background

• When the Anaconda installer initializes conda, it appends a snippet at the end of the ~/.bashrc file. This file is executed each time the user opens bash interactively. The snippet allows the user to run conda commands (ie conda activate my_env) from bash.

• Anaconda installer v2020.02 appended the following conda snippet in ~/.bashrc:

# >>> conda initialize >>>
# !! Contents within this block are managed by 'conda init' !!
__conda_setup="$('/opt/anaconda3/bin/conda' 'shell.bash' 'hook' 2> /dev/null)"
if [ $? -eq 0 ]; then
    eval "$__conda_setup"
else
    if [ -f "/opt/anaconda3/etc/profile.d/conda.sh" ]; then
        . "/opt/anaconda3/etc/profile.d/conda.sh"
    else
        export PATH="/opt/anaconda3/bin:$PATH"
    fi
fi
unset __conda_setup
# <<< conda initialize <<<

• The path /opt/anaconda3/ to be replaced with the correct reference: usually /home/USERNAME/anaconda3/.

The problem

Sourcing ~/.bashrc in crontab -e won't work (at least not on Ubuntu).

Explanation:

• On Ubuntu, ~/.bashrc has the following (or similar) line at the beginning of the file:

# If not running interactively, don't do anything
[ -z "$PS1" ] && return

• This means that if we try to source the ~/.bashrc file in crontab, the rest of the .bashrc file will not execute because crontab is not running interactively (see another post on this topic). Which means that the conda snippet mentioned above will never get executed by crontab even if we source ~/.bashrc.

_________ Working solution _________

The solution I have found is to copy the conda snippet to a separate file.

1. Copying the conda snippet from ~/.bashrc to ~/.bashrc_conda

Copy the snippet mentioned above to another file, for example ~/.bashrc_conda.

Ensure that:

• The user running the cronjob has permission to read this file.
• Other users cannot write to this file (security risk).

2. In crontab -e insert 2 lines to run bash instead of sh and to source ~/.bashrc_conda

Run crontab -e and add the following 2 lines before the cronjob:

SHELL=/bin/bash
BASH_ENV=~/.bashrc_conda

Explanation:

• SHELL=/bin/bash means that crontab will run the cronjobs via bash instead of sh (default). See post.

• BASH_ENV=~/.bashrc_conda sources the conda snippet to bash run by chrontab. See post and post.

3. In crontab -e insert in the cronjob line conda activate my_env; before the desired .py script execution

Example of entry for a script that would execute at noon 12:30 each day within the desired conda environment:

30 12 * * * conda activate my_env; python /path/to/script.py

Notice conda activate my_env; before the command to run the Python interpreter.

_______________

And voilà, it worked.

Any downsides?

If the conda snippet in .bashrc gets updated by a conda update, it will of course not be reflected in the separate .bashrc_conda file. One may need to check for updates from time to time.

One could also to append ; conda deactivate at the end of that cronjob, but this may be redundant.

I recently switched from canopy to Anaconda precisely to get away from having to activate an env in cron jobs. Anaconda makes this very simple, based on the PATH enviornment variable. (I'm using miniconda not the full Anaconds install but I believe anaconda should work the same way)

There are two different approaches, I've tested;

• Add a shebang in your python script, main.py

  #!/home/users/user_name/miniconda2/envs/my_env/bin/python

• Add PATH to the top of your crontab

  PATH=/home/users/user_name/miniconda2/envs/my_env/bin

Update:

Jérôme's answer and cbarrick's comments are correct. I just got burned using the above approach in a Conda env which needed pynco, which needs the full conda environment to find proper the nco commands, such as ncks, ncrcat. Solved by running a bash script from cron which calls conda activate first.

Don't call sh but bash. source is a bash command.

    - sh scripts/my_script.bash
    + bash scripts/my_script.bash

Or just

    chmod +x scripts/my_script.bash
    ./scripts/my_script.bash

since you added the bash shebang.