How can you "clone" a conda environment into the root environment?

To make a copy of your root environment (named base), you can use following command; worked for me with Anaconda3-5.0.1:

conda create --name <env_name> --clone base

you can list all the packages installed in conda environment with following command

conda list -n <env_name>

There are options to copy dependency names/urls/versions to files.

Recommendation

Normally it is safer to work from a new environment rather than changing root. However, consider backing up your existing environments before attempting changes. Verify the desired outcome by testing these commands in a demo environment. To backup your root env for example:

λ conda activate root
λ conda env export > environment_root.yml
λ conda list --explicit > spec_file_root.txt

Options

Option 1 - YAML file

Within the second environment (e.g. myenv), export names⁺ to a yaml file:

λ activate myenv
λ conda env export > environment.yml  

then update the first environment⁺ (e.g. root) with the yaml file:

λ conda env update --name root --file environment.yml     

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Option 2 - Cloning an environment

Use the --clone flag to clone environments (see @DevC's post):

λ conda create --name myclone --clone root

This basically creates a direct copy of an environment.

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Option 3 - Spec file

Make a spec-file⁺⁺ to append dependencies from an env (see @Ormetrom):

λ activate myenv
λ conda list --explicit > spec_file.txt
λ conda install --name root --file spec_file.txt

Alternatively, replicate a new environment (recommended):

λ conda create --name myenv2 --file spec_file.txt

See Also

• conda env for more details on the env sub-commands.
• Anaconada Navigator desktop program for a more graphical experience.
• Docs on updated commands. With older conda versions use activate (Windows) and source activate (Linux/Mac OS). Newer versions of conda can use conda activate (this may require some setup with your shell configuration via conda init).
• Discussion on keeping conda env

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Extras

There appears to be an undocumented conda run option to help execute commands in specific environments.

# New command
λ conda run --name myenv conda list --explicit > spec_file.txt

The latter command is effective at running commands in environments without the activation/deactivation steps. See the equivalent command below:

# Equivalent
λ activate myenv
λ conda list --explicit > spec_file.txt
λ deactivate

Note, this is likely an experimental feature, so this may not be appropriate in production until official adoption into the public API.

^{+Conda docs have changed since the original post; links updated.++Spec-files only work with environments created on the same OS. Unlike the first two options, spec-files only capture links to conda dependencies; pip dependencies are not included.}

When setting up a new environment and I need the packages from the base environment in my new one (which is often the case) I am building in the prompt a identical conda environment by using a spec-file.txt with:

conda list --explicit > spec-file.txt

The spec-file includes the packages of for example the base environment.

Then using the prompt I install the the packages into the new environment:

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

The packages from base are then available in the new environment.

The whole process is describe in the doc: https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html#building-identical-conda-environments