3.5.2. Installing Conda#

A minimal installation of Conda can be setup by installing Miniconda. You will need to download and run the Miniconda installer following the steps below.

1. Downloading Miniconda#

To download the correct version of Miniconda:

  1. Open the Conda downloads page in a browser.

  2. Navigate to the Linux installers section (Fig. 63)

    Miniconda installers for Linux

    Fig. 63 Miniconda installers for Linux#

  3. Click on the download link corresponding to:

    Python 3.8 — Miniconda3 Linux 64-bit

    Save the file. It will be saved as:



    You can verify the file’s SHA256 checksum to ensure it has been downloaded correctly. How?

2. Running the installer#

Run the installer using the bash command:

bash Miniconda3-latest-Linux-x86_64.sh

This will print a welcome message:

Welcome to Miniconda3 py38_4.8.3

In order to continue the installation process, please
review the license agreement.
Please, press ENTER to continue

3. Reviewing licence agreement#

Press the ENTER key to view the licence agreement. Scroll down to read the licence. Towards the end, you will notice a prompt:

Do you accept the license terms? [yes|no]
[no] >>> yes

You will need to type yes to accept the agreement and then press the ENTER key to proceed.

4. Confirming Miniconda install location#

Next, you will be asked to provide a path to install Miniconda.

Miniconda3 will now be installed into this location:

  - Press ENTER to confirm the location
  - Press CTRL-C to abort the installation
  - Or specify a different location below

[/home/user/miniconda3] >>>

Press ENTER here to accept the default value.

Installation will now proceed. When complete, you will notice a prompt asking if you would like to initialize Miniconda 3.

Do you wish the installer to initialize Miniconda3
by running conda init? [yes|no]
[no] >>> yes

Type yes and then press the ENTER key. This will add the conda command to your $PATH.

As a result of this configuration, Conda base environment will be activated automatically when you open a terminal session. This can be disabled in the next step. Why?

5. Disabling auto-activation of base environment#

Open a new terminal. Your shell prompt should now appear like the following:

(base) user@cookbook:~$

The (base) label at the beginning of the prompt, indicates that Conda base environment is now active.

To disable this behaviour, so you can activate the environment manually when you need it, run the following command:

conda config --set auto_activate_base false

6. Setting up channels#

Channels provide additional software for Conda.

Conda’s configuration includes a defaults channel. The bioconda and conda-forge channels can also be added to access an even larger collection of software. The bioconda channel, for example, provides over 7000 packages of Bioinformatics software.

To add these channels to your configuration, you can run the commands below.


You will need to run these commands in the same order as given below.

conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge

Installation and configuration of Conda is now complete.

You can now start using Conda to create environments and install packages from repositories.