Scientific computing at AMAP

Using conda at AMAP

Recently, Anaconda has updated its terms of services for academia and research. As being part of research institutes of more that 200 persons, we are now subject to a licensing fee to use Anaconda products. However, we can still use the conda tool.

While the conda tools is free and open-source, Anaconda (a graphical interface that uses conda) is a licensed product.

Also, conda uses “channels” to gets access to software and librairies. Some are licensed and managed by Anaconda while other are free and open.

Let’s see how to keep using conda at AMAP, and what you should be aware of.

Installations of conda distributions

There exist multiple distributions of conda that you can use, cf. here.

What you should avoid:

  • using the Anaconda distribution, as it is a licensed product. If you have it installed, you should uninstall it and consider other options below. Make sure you keep your existing environments.
  • using the miniconda distribution. Although it is free to use, you should avoid this option as the default channels are managed under Anconda licensing. However, you can still use miniconda if you configure it properly.

What you should do:

  • use the miniforge distribution. It is free to use and is configured to use conda-forge as the default channel (which is free too). This is the recommended distribution to use at AMAP.

Licensed channels

Licensed channels are channels that are managed by Anaconda and are subject to licensing fees. You should avoid using these channels.

You can check the full list of licensed channels here.

The main one is the defaults channel, which includes the following sub-channels: r, main and msys2.

You need to remove these channels from your configuration.

Note

It is very unlikely that you won’t find any packages in the conda-forge channel that you were using in the defaults channel. This change should not affect your workflow.

Important

CIRAD has decided to ban the access to these licensed channels on their network, which means your conda will throw an error if you try to access them when you are physically located at CIRAD, or using their VPN.

Check configuration

As you may have installed miniconda before all this licensing issue (remember, if you have installed Anaconda: you should uninstall it and install miniforge instead!), you need to check your configuration.

conda config --show channels

and if any of the channels are licensed, you should remove them (here we remove the defaults channel):

conda config --remove channels defaults
conda config --show channels

You should now see only the conda-forge channel. If you want to add extra (free) channels:

conda config --add channels conda-forge #if not already present
conda config --add channels bioconda
Note

For additional configuration, you might want to add the following lines:

conda config --set channel_priority strict #usefull to avoid conflicts and speed up the resolution of dependencies
conda config --add channels nodefaults #usefull when you want to share environments

Configuration at AMAP

As mentioned earlier, CIRAD has decided to ban the access to licensed channels on their network. But to keep access to the free channels, you now need a certificate to access the free repositories.

  1. Download the certificate Click to Download.
  2. Copy the certificate anywhere in your computer where you can access it. miniforge installation folder is probably a good place.
  3. conda config --set ssl_verify <path_to_certificate>

Without this extra configuration step, you won’t be able to use conda at AMAP / CIRAD.

Resources

  • mivegec lab publish an extensive and well done summary of the situation at IRD in Montpellier here.
  • INRAE has published some recommandations for using conda here
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