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Conda and Mamba

Both the miniconda3 and minforge modules include only conda, python, and a few other packages. Only the miniforge module provides mamba.

Mamba is a drop-in replacement of conda, and is faster at resolving dependencies than conda. For commands like conda install and conda search, condacan be replaced with mambaon Oscar. More details can be found in Mamba User Guide.

Conda Initialization

It is not recommended to initialize conda via conda init.

Access Conda via Modules

To access the conda or mamba command, load either a miniconda3 or miniforge module and then run the source commandl

module load miniconda3/23.11.0s

source /oscar/runtime/software/external/miniconda3/23.11.0/etc/profile.d/conda.sh

Conda Environment

A user may install all needed software packages for a project in a conda environment. A conda environment can be

  • shared among all users if the environment is installed in a shared directory

  • private to one user if the environment is installed in a user's private directory

The command 'conda info' shows important configurations for conda environment.

$ conda info 

     active environment : None
            shell level : 0
       user config file : /users/yliu385/.condarc
 populated config files : /users/yliu385/.condarc
          conda version : 23.1.0
    conda-build version : not installed
         python version : 3.10.9.final.0
       virtual packages : __archspec=1=x86_64
                          __glibc=2.34=0
                          __linux=5.14.0=0
                          __unix=0=0
       base environment : /oscar/runtime/software/external/miniconda3/23.11.0  (writable)
      conda av data dir : /oscar/runtime/software/external/miniconda3/23.11.0/etc/conda
  conda av metadata url : None
           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
          package cache : /oscar/runtime/software/external/miniconda3/23.11.0/pkgs
                          /users/yliu385/.conda/pkgs
       envs directories : /oscar/runtime/software/external/miniconda3/23.11.0/envs
                          /users/yliu385/.conda/envs
               platform : linux-64
             user-agent : conda/23.1.0 requests/2.28.1 CPython/3.10.9 Linux/5.14.0-284.11.1.el9_2.x86_64 rhel/9.2 glibc/2.34
                UID:GID : 140348764:2128288
             netrc file : None
           offline mode : False

Below are some important configurations:

  • envs directories: a list of directories where a conda environment is installed by default. In the output of 'conda info' above, the first default directory to install a conda environment is a $HOME/anaconda.

  • package cache: a list of directories where downloaded packages are stored.

Create a New Conda Environment

To create a new conda environment in a default directory, run the following command:

conda create -n conda_environment_name

To create a new conda environment in a different directory, run the following command:

conda create -p  /path/to/install/conda_environment_name

Activate a Conda Environment

After creating a conda environment, users can activate a conda environment to install or access packages in the environment via the following command. 

conda activate conda_environment_name

The commands above will only work if:

  • A conda environment with the specified name (conda_environment_name in the example) exists

  • The appropriate anaconda module has been loaded (if you are unsure about this one, consult this documentation)

If you need to activate a conda environment in a bash script, you need to source the conda.sh as shown in the following example bash script:

module load miniconda3/23.11.0s

source /oscar/runtime/software/external/miniconda3/23.11.0/etc/profile.d/conda.sh

conda activate my_env

After installing packages in an active environment (instructions below), you do not need to load or install those packages in the bash script; any packages installed in the conda environment (before the script even starts) will be available through the environment after it is activated (line 4 in the code above).

Do NOT activate a conda environment before submitting a batch job if the batch job activates a conda environment. Otherwise, the batch job will not be able to activate the conda environment and hence fail.

To deactivate a conda environment, simply use the following command:

conda deactivate

Install Packages in an Active Conda Environment

To install a package, we need to first activate a conda environment, and then run

conda install package_name=version

The "=version" is optional. By default, conda install a package from the anaconda channel. To install a package from a different channel, run conda install with the -c option. For example, to install a package from the bioconda channel, run

conda install -c bioconda package_name

Delete a Conda Environment

To delete a conda environment, run

conda env remove -n conda_environment_name

Remove Caches

Conda may download lots of additional packages when installing a package. A user may use up all quota due to these downloaded packages. To remove the downloaded packges, run

conda clean --all

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