Replacing an existing Conda installation

Due to changes in software and licensing, you may wish to replace your current installation of conda with a different version such as Miniforge. There are three different ways to maintain your environments during this change: using the conda "clone" feature, build a new identical environment, or by modifying .condarc.

This guide assumes you have installed a new conda version into a different directory than your existing installation, e.g. your current installation is in the directory ~/miniconda3 and you install Miniforge into ~/miniforge3.

Warning

As you go through this guide, regularly use the command which conda to make sure you are using the correct installation for each command.

Using conda --clone

First, check that you are using your new conda version by running

which conda

in your terminal, logged on to an HPCC dev node.

Then, you can run the clone command:

conda create --name myclone --clone /path/to/myenv

where myclone is the name of your copy, and /path/to/myenv is the full path to the environment you want to copy e.g. /mnt/home/MyMSUID/miniconda3/myenv.

You can repeat this for all of your existing environments. Once you have completed the process, you can delete your previous conda version entirely.

Warning

Check that you have enough file space and file count available to make full copies of your old environments using the quota command.

Using conda list

To build an identical environment with the same packages as the original, activate your original conda version. Check that you are using your original conda version by running

which conda

in your terminal, logged on to an HPCC dev node.

Then activate the environment you want to export. Then run

conda env export --no-builds > spec-file.yml

where spec-file.yml is a file containing the precise packages used to build your environment.

Deactivate your original conda version.

Then, activate your new conda version and run the command

conda create --name myenv --file spec-file.yml

which will create a new environment named myenv with the same package list. You can repeat this for all of your existing environments. Once you have completed the process, you can delete your previous conda version entirely.

Note

If you are low on space, you can create the specification files, then delete the old conda installation before creating the new environments. Make sure you try out the specification file process to ensure it works for your new conda version.

Modifying .condarc

Note

This also works for conda environments in research spaces!

To avoid duplicating environments or downloading packages, you can point your new conda version at your old environments by using the .condarc settings file.

First, check that you are using your new conda version by running

which conda

in your terminal, logged on to an HPCC dev node.

Then, run the command

conda config --append envs_dirs /path/to/old/envs

where /path/to/old/envs is the path to your original environments e.g. /mnt/home/MyMSUID/miniconda3/envs. You can find this path by running conda env list using your old conda version, which will produce output like this:

# conda environments:
#
base                     /mnt/home/MyMSUID/miniconda3
myenv                   /mnt/home/MyMSUID/miniconda3/envs/myenv

You can check that the path in .condarc is correct by running more .condarc in your home directory. The output should look like:

envs_dirs:
  - /mnt/home/MyMSUID/miniconda3/envs

and then run conda env list using your new conda version, which should produce output like this:

# conda environments:
#
base                     /mnt/home/MyMSUID/miniforge3
myenv                   /mnt/home/MyMSUID/miniconda3/envs/myenv

Note how base is in the new conda version, while myenv is the old path. You can then activate the old environment using the new version with conda activate myenv as usual.