Selecting the channels for package installation
In the Mamba module, you can use only the following channels:
conda-forge
bioconda
The channels provided by Anaconda, Inc. (default and anaconda channels) have a service fee.
Package installation with specified channels
You can specify channels in the package installation with the -c conda-forge command.
username@lanta:~> conda install -c conda-forge matplotlib
Verifying the default channel URLs within your conda module
You can use the conda info command to view the default channel URLs.
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.
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.