Conda¶
Description¶
The tool conda is a package manager that lets you to install some libraries and softwares in compartmentalized environments. Here we'll be using the miniforge distribution that has the following advantages:
- like miniconda, and unlike Anaconda, it only contains the minimum requirements to operate,
- it bans the Anaconda distribution channels that may cause some billing problems and replaces them by channels from conda-forge.
Objectives¶
Configure and use conda on the cluster by using the version available with the modules.
Remark
This documentation is written for conda installed by Genotoul-Bioinfo platform. You can use this documentation with another installation, but some parts may not apply to it.
How to?¶
- Configure
condaon the cluster - Create a conda environment
- List environments and activate one
- Modify an environment
- Reproducible environments (export and import an environment)
- Delete an environment and clean files managed by conda
- Troubleshootings Common errors with conda on cluster.
TL;DR¶
Prerequisites
Configure conda the first time you use it on the cluster, else you may block your account by filling your $HOME directory.
Load the Miniforge3 module and use following commands:
# Activate the env# /!\ This command differs from the usual 'conda activate' command /!\source activate <env># Do something with env...
# Deactivate the envconda deactivate
Activation command
On the cluster, environment activation uses the command source activate <env> instead of conda activate <env>.