Migrating from Miniconda to Mamba

1 Loading Mamba module
2 Selecting the channels for package installation
3 Verifying the default channel URLs within your conda module
4 Verifying the user config file for your conda module
5 Installing package with specified channels

Loading Mamba module

Use the ml av Mamba command to see which version of Mamba is available on the LANTA HPC system.
Use the ml Mamba/xx.xx.x command to load the Mamba version that you want to use. If you don't specify a version, the default version (D) is loaded, which is Mamba/23.11.0-0.

username@lanta:~> ml av Mamba
---------------------- /lustrefs/disk/modules/easybuild/modules/all -----------------------
   Mamba/23.11.0-0 (D)
Use "module spider" to find all possible modules and extensions.
Use "module keyword key1 key2 ..." to search for all possible modules matching any of the "keys".
username@lanta:~> ml Mamba/23.11.0-0

Selecting the channels for package installation

In the Mamba module, you can use only the free channels, such as:

conda-forge
bioconda

The channels provided by Anaconda, Inc. (default and anaconda channels) have a service fee.

Verifying the default channel URLs within your conda module

You can use the conda info command to view the default channel URLs.

username@lanta:~> ml Mamba/23.11.0-0
username@lanta:~> conda info
     active environment : None
            shell level : 0
       user config file : /home/username/.condarc
 populated config files : /lustrefs/disk/modules/easybuild/software/Mamba/23.11.0-0/.condarc
          conda version : 23.11.0
    conda-build version : not installed
         python version : 3.10.13.final.0
                 solver : libmamba (default)
       virtual packages : __archspec=1=zen3
                          __conda=23.11.0=0
                          __glibc=2.31=0
                          __linux=5.14.21=0
                          __unix=0=0
       base environment : /lustrefs/disk/modules/easybuild/software/Mamba/23.11.0-0  (read only)
      conda av data dir : /lustrefs/disk/modules/easybuild/software/Mamba/23.11.0-0/etc/conda
  conda av metadata url : None
           channel URLs : https://conda.anaconda.org/conda-forge/linux-64
                          https://conda.anaconda.org/conda-forge/noarch
          package cache : /lustrefs/disk/modules/easybuild/software/Mamba/23.11.0-0/pkgs
                          /home/ywongnon/.conda/pkgs
       envs directories : /home/ywongnon/.conda/envs
                          /lustrefs/disk/modules/easybuild/software/Mamba/23.11.0-0/envs
               platform : linux-64
             user-agent : conda/23.11.0 requests/2.31.0 CPython/3.10.13 Linux/5.14.21-150400.24.81_12.0.86-cray_shasta_c sles/15.4 glibc/2.31 solver/libmamba conda-libmamba-solver/23.12.0 libmambapy/1.5.5
                UID:GID : 1980400170:1980400170
             netrc file : None
           offline mode : False

You can observe two URLs for the conda-forge channel above.

channel URLs : https://conda.anaconda.org/conda-forge/linux-64
               https://conda.anaconda.org/conda-forge/noarch

When you add the bioconda channel to your conda module, you will notice that there are four URLs listed for the conda-forge and bioconda channels.

However, if you found the URLs in this format, you need to check your user config file. To access the below channels, a license from Anaconda, Inc. is required.

Verifying the user config file for your conda module

When using the conda info command, you can view the directory path of the user config file.

After that, you can use the cat /home/username/.condarc command to view your configuration.

If the default and anaconda channels are present in your user config file, kindly remove them.

Installing package with specified channels

You can specify channels in the package installation with the -c option command.

For example,