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.
channel URLs : https://conda.anaconda.org/conda-forge/linux-64
https://conda.anaconda.org/conda-forge/noarch
https://conda.anaconda.org/bioconda/linux-64
https://conda.anaconda.org/bioconda/noarch
However, if you found the URLs in this format, you need to check your user config file. To access below channels, license from Anaconda Inc. is required.
channel URLs : https://repo.anaconda.com/pkgs/main/linux-64
https://repo.anaconda.com/pkgs/main/noarch
https://repo.anaconda.com/pkgs/r/linux-64
https://repo.anaconda.com/pkgs/r/noarch
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.
user config file : /home/username/.condarc
After that, you can use the cat /home/username/.condarc command to view your configuration.
username@lanta:~> cat /home/username/.condarc channels: - conda-forge - bioconda channel_priority: strict
If the default and anaconda channels are present in your user config file, kindly remove them.
Package installation with specified channels
You can specify channels in the package installation with the -c conda-forge command.
username@lanta:~> ml Mamba/23.11.0-0 username@lanta:~> conda activate your_env username@lanta:~> conda install -c conda-forge matplotlib