# Conda and Mamba

The minforge modules include only conda, python, mamba and a few other packages.

Mamba is a drop-in replacement of conda, and is faster at resolving dependencies than conda. For commands like `conda install` and `conda search`, `conda`can be replaced with `mamba`on Oscar. More details can be found in [Mamba User Guide](https://mamba.readthedocs.io/en/latest/user_guide/mamba.html).

## Conda Initialization

It is not recommended to initialize conda via `conda init`.

## Access Conda via Modules

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

```bash
module load miniforge3/25.3.0-3
source ${MAMBA_ROOT_PREFIX}/etc/profile.d/conda.sh
```

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

```console
$ conda info

     active environment : None
            shell level : 0
       user config file : /users/yliu385/.condarc
 populated config files : /oscar/rt/9.6/25/x86_64_v3/miniforge3-25.3.0-3-a6hhdjzejtacz63sugjqnvgosfqz63ul/.condarc
                          /users/yliu385/.condarc
          conda version : 25.3.0
    conda-build version : not installed
         python version : 3.12.10.final.0
                 solver : libmamba (default)
       virtual packages : __archspec=1=cascadelake
                          __conda=25.3.0=0
                          __glibc=2.34=0
                          __linux=5.14.0=0
                          __unix=0=0
       base environment : /oscar/rt/9.6/25/x86_64_v3/miniforge3-25.3.0-3-a6hhdjzejtacz63sugjqnvgosfqz63ul  (writable)
      conda av data dir : /oscar/rt/9.6/25/x86_64_v3/miniforge3-25.3.0-3-a6hhdjzejtacz63sugjqnvgosfqz63ul/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 : /oscar/rt/9.6/25/x86_64_v3/miniforge3-25.3.0-3-a6hhdjzejtacz63sugjqnvgosfqz63ul/pkgs
                          /users/yliu385/.conda/pkgs
       envs directories : /oscar/rt/9.6/25/x86_64_v3/miniforge3-25.3.0-3-a6hhdjzejtacz63sugjqnvgosfqz63ul/envs
                          /users/yliu385/.conda/envs
               platform : linux-64
             user-agent : conda/25.3.0 requests/2.32.3 CPython/3.12.10 Linux/5.14.0-570.62.1.0.1.el9_6.x86_64 oracle/9.6 glibc/2.34 solver/libmamba conda-libmamba-solver/25.3.0 libmambapy/2.1.1
                UID:GID : 140348764:601
             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:

```bash
conda create -n conda_environment_name
```

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

```bash
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.

```bash
conda activate conda_environment_name
```

{% hint style="info" %}
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](https://docs.ccv.brown.edu/oscar/software/modules))
  {% endhint %}

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:

```bash
module load miniforge3/25.3.0-3
source ${MAMBA_ROOT_PREFIX}/etc/profile.d/conda.shetc/profile.d/conda.sh
conda activate my_env
```

{% hint style="info" %}
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 3 in the code above).
{% endhint %}

{% hint style="danger" %}
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.
{% endhint %}

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

```bash
conda deactivate
```

### Install Packages in an Active Conda Environment

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

{% tabs %}
{% tab title="Conda" %}

```bash
conda install package_name=version
```

{% endtab %}

{% tab title="Mamba" %}

```bash
mamba install package_name=version`
```

{% endtab %}
{% endtabs %}

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

{% tabs %}
{% tab title="Conda" %}

```bash
conda  install -c bioconda package_name
```

{% endtab %}

{% tab title="Mamba" %}

```bash
mamba install -c bioconda package_name
```

{% endtab %}
{% endtabs %}

### Delete a Conda Environment

To delete a conda environment, run

```bash
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

```bash
conda clean --all
```


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