Migrating your conda setup

If you use a compute cluster and you use conda, the default location for your conda environments will be in your home directory. This can be annoying for a couple reasons:

  • Your home directory might have a storage quota
  • Collaborators won't have access to your environments

Fortunately, it's pretty easy to migrate your setup to a new directory (like a lab share).

Export (and delete) existing environments

For each environment you want to export it's as simple as
conda activate my_environ, followed by conda env export > my_environ.yml and conda remove --name my_environ --all

Tweak your ~/.bash_profile/~/.bashrc

conda is always changing how this works, but doing something like this worked for me. Make sure to 1. back up your ~/.bashrc/~/.bash_profile
line like and 2. remove anything else conda related you find in either of those files:

If your .bash_profile contains something like:

if [ -f ~/.bashrc ]; then
        . ~/.bashrc
fi

you'll want to put the following in .bashrc, otherwise you'll want to put it in your .bash_profile :


#conda activate
#. /project2/xinhe/software/miniconda3/etc/profile.d/conda.sh
# added by Miniconda3 4.5.12 installer
# >>> conda init >>>
# !! Contents within this block are managed by 'conda init' !!
__conda_setup="$(CONDA_REPORT_ERRORS=false '/project2/xinhe/software/miniconda3/bin/conda' shell.bash hook 2> /dev/null)"
if [ $? -eq 0 ]; then
    \eval "$__conda_setup"
else
    if [ -f "/project2/xinhe/software/miniconda3/etc/profile.d/conda.sh" ]; then
        . "/project2/xinhe/software/miniconda3/etc/profile.d/conda.sh"
        CONDA_CHANGEPS1=false conda activate base
    else
        \export PATH="/project2/xinhe/software/miniconda3/bin:$PATH"
    fi
fi
unset __conda_setup
# <<< conda init <<<

#put the root conda environment first
echo "$PATH"|grep -vq "^/project2/xinhe/software/miniconda3/bin" && export PATH="/project2/xinhe/software/miniconda3/bin:$PATH"

Last steps

Log off and then log in again, and make sure that which conda looks like /project2/xinhe/software/miniconda3/bin/conda,
then reinstall each of your conda environments:

conda env create -f my_environ.yml

You'll want to make sure that ~/.conda/environments.txt contains the paths to your environments in their new directories and not the old ones.

That's it!