Goal: Introduce how conda environments can be reproduced and shared.
Based on Managing Environments.
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In the following examples, we assume you already have a |
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Clone an Environment
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Existing Conda environments can be cloned (essentially copied). |
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[salexan5@mblog2 ~]$ 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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Example
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[salexan5@mblog2 software]$ conda create -p py_env2 --clone py_env Retrieving notices: ...working... done Source: /home/salexan5<username>/.conda/envs/py_env Destination: /cluster/medbow/project/arcc<project-name>/salexan5<username>/software/py_env2 Packages: 39 Files: 1 ... # # To activate this environment, use # $ conda activate /cluster/medbow/project/arcc<project-name>/salexan5<username>/software/py_env2 |
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Notice: The source (environment being cloned) and the destination (new cloned environment) are listed. In the above, we are using the |
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Notice how you need to activate/use this cloned environment: |
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[salexan5@mblog2 ~]$ cat ~/.conda/environments.txt /home/salexan5<username>/.conda/envs/py_env /project/arcc<project-name>/salexan5<username>/conda/envs/r_env /cluster/medbow/project/arcc<project-name>/salexan5<username>/software/slim_env_4.2.2 /cluster/medbow/project/arcc<project-name>/salexan5<username>/software/py_env2 [salexan5@mblog2 ~]$ conda info --env # conda environments: # base /apps/u/opt/linux/miniconda3/24.3.0 /cluster/medbow/project/arcc<project-name>/salexan5<username>/software/py_env2 /cluster/medbow/project/arcc<project-name>/salexan5<username>/software/slim_env_4.2.2 py_env /home/salexan5<username>/.conda/envs/py_env r_env /project/arcc<project-name>/salexan5<username>/conda/envs/r_env |
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Need to define the full path to activate. |
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[salexan5@mblog2 ~]$ conda activate /cluster/medbow/project/arcc<project-name>/salexan5<username>/software/py_env2 (/cluster/medbow/project/arcc<project-name>/salexan5<username>/software/py_env2) [salexan5@mblog2 ~]$ |
Export an Environment
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[salexan5@mblog2 ~]$ conda activate r_env
(r_env) [salexan5@mblog2 ~]$ conda env export > r_env.yml
(r_env) [salexan5@mblog2 ~]$ conda deactivate
[salexan5@mblog2 ~]$ cat r_env.yml
name: r_env
channels:
- conda-forge
- defaults
dependencies:
- _libgcc_mutex=0.1=main
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- zstd=1.5.5=hc292b87_2
prefix: /project/arcc/salexan5/conda/envs/r_env |
Conda env command
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Conda env command
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The |
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[]$ 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
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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 |
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[]$ 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
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Using the |
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[salexan5@mblog2 software]$ cd /project/<project-name>/<username>/software/ []$ conda env create -p r_env2 --file r_env.yml ... # # To activate this environment, use # # $ conda activate /cluster/medbow/project/arcc<project-name>/salexan5<username>/software/r_env2 ... |
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