vuthanhdatt's Second Brain

Crontab

1 min read

cron job to run under conda virtual environment

1. Copy snippet appended by Anaconda in ~/.bashrc (at the end of the file) to a separate file ~/.bashrc_conda

As of Anaconda 2020.02 installation, the snippet reads as follows:

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

In crontab -e add lines to run cronjobs on bash and to source ~/.bashrc_conda

Run crontab -e and insert the following before the cronjob:

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

In crontab -e include at beginning of the cronjob conda activate my_env; as in example

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

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

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