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Table of Contents
stylenone

Clone an Environment

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Note

In the following examples, we assume you already have a miniconda3 module already loaded.

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Clone an Environment

Info

Existing Conda environments can be cloned (essentially copied).

Code Block
[]$ conda create --help
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options:
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  --clone ENV           Create a new environment as a copy of an existing local environment.
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Code Block
[]$ conda create -p py_env2 --clone py_env
Retrieving notices: ...working... done
Source:      /home/<username>/.conda/envs/py_env
Destination: /cluster/medbow/project/<project-name>/<username>/software/py_env2
Packages: 39
Files: 1
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#
# To activate this environment, use
#     $ conda activate /cluster/medbow/project/<project-name>/<username>/software/py_env2
Info

Notice: The source (environment being cloned) and the destination (new cloned environment) are listed.

In the above, we are using the -p option so the destination is within the current working directory, and cloning from an existing environment that was created within the default environment location - so only its name (not absolute path) is required.

Expand
titleFull Details:
Code Block
[]$ pwd
/project/<project-name>/<username>/software
[]$ ls
slim_env_4.2.2

[]$ conda create -p py_env2 --clone py_env
Retrieving notices: ...working... done
Source:      /home/<username>/.conda/envs/py_env
Destination: /cluster/medbow/project/<project-name>/<username>/software/py_env2
Packages: 39
Files: 1

Downloading and Extracting Packages:


Downloading and Extracting Packages:

Preparing transaction: done
Verifying transaction: done
Executing transaction: done
#
# To activate this environment, use
#
#     $ conda activate /cluster/medbow/project/<project-name>/<username>/software/py_env2
#
# To deactivate an active environment, use
#
#     $ conda deactivate


[]$ ls
py_env2  slim_env_4.2.2

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Code Block
[]$ conda activate /cluster/medbow/project/<project-name>/<username>/software/py_env2
(/cluster/medbow/project/<project-name>/<username>/software/py_env2) []$

Export an Environment

Code Block
[]$ conda activate r_env
(r_env) []$ conda env export > r_env.yml
(r_env) []$ conda deactivate

[]$ cat r_env.yml
name: r_env
channels:
  - conda-forge
  - defaults
dependencies:
  - _libgcc_mutex=0.1=main
...
  - zstd=1.5.5=hc292b87_2
prefix: /project/<project-name>/<username>/conda/envs/r_env

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Conda env commandConda env command

Info

The env sub-command provides the a process that can be used to export into a readable text file a description of the entire Conda environment that can then used to create (essentially import) to replicate.

Code Block
[]$ conda env --help
usage: conda env [-h] command ...

positional arguments:
  command
    config    Configure a conda environment.
    create    Create an environment based on an environment definition file.
    export    Export a given environment
    list      List the Conda environments.
    remove    Remove an environment.
    update    Update the current environment based on environment file.

options:
  -h, --help  Show this help message and exit.

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Export an Environment

Info

Within an active environment we can export into a readable file a description of the entire Conda environment. This describes all the system related libraries as well as anything that that was explicitly conda install-ed.

Code Block
[]$ conda activate r_env
(r_env) []$ conda env export > r_env.yml
(r_env) []$ conda deactivate

[]$ cat r_env.yml
name: r_env
channels:
  - conda-forge
  - defaults
dependencies:
  - _libgcc_mutex=0.1=main
...
  - zstd=1.5.5=hc292b87_2
prefix: /project/<project-name>/<username>/conda/envs/r_env

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Import an Environment

Info

Using the env create sub-command we can then define a file to read/import that describes the environment we want to create - essentially cloning it.

Code Block
[]$ cd /project/<project-name>/<username>/software/
[]$ conda env create -p r_env2 --file r_env.yml
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#
# To activate this environment, use
#
#     $ conda activate /cluster/medbow/project/<project-name>/<username>/software/r_env2
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