Install Miniconda

Installing the Conda package management system.

Download the installer #

In a new Terminal application, log into the CCB cluster.

Download the latest Miniconda installer for Linux using the following command.

wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh

For reference, the URL to the installer file in the command above was obtained from the Latest Miniconda installer links.

Run the installer #

Use bash to execute the installer file as demonstrated below.

bash Miniconda3-latest-Linux-x86_64.sh -b -p ~/conda

Note the use of options to control the behaviour of the installer:

• The option -b runs the installer in ‘batch’ mode (without manual intervention). This assumes that you agree to the license agreement. It also prevents the installer from modifying your ~/.bashrc file.
• The option -p specifies the installation path, the location where Conda will be installed. We recommend specifying ~/conda, which will create a directory conda in your home directory.

Once the installation successfully completes, you may want to delete the installer file.

rm Miniconda3-latest-Linux-x86_64.sh

Test the installation #

Before going further, we recommend testing that the new installation of Conda works as expected.

source ~/conda/etc/profile.d/conda.sh
conda activate base

First, the source command executes a script that makes Conda discoverable in the Bash environment of your Terminal application. This command is not expected to return any information in the Terminal.

Then, the conda command is used to activate the base environment that was created during the installation process. Again, this command is not expected to return any information in the Terminal. However, after that command completes, the prefix (base) should be visible at the start of the prompt.

The which command can also be used to verify that the conda command is found on the PATH, at the expected location.

which conda

Deactivate the environment #

Before going further, we recommend deactivating the base environment.

To do so, the conda command is used with the deactivate sub-command.

conda deactivate

Create a shortcut #

Open your ~/.bashrc file and add the following lines.

# Create an alias to activate the Conda base environment
alias conda_activate_base='source ~/conda/etc/profile.d/conda.sh && conda activate base'

Test the shortcut #

Run the following lines of code sequentially.

source ~/.bashrc
conda_activate_base

First, the source command is used to execute the commands in ~/.bashrc file, including the alias command that defines the new shortcut.

Then, the newly defined alias is used to invoke the command that is now assigned to it. This shortcut should have the same effect as typing the full command defined in the alias, activating the base Conda environment and adding the (base) prefix to the prompt.

Next steps #

From this point, new instances of the Terminal application will automatically execute the ~/.bashrc file and define the alias as soon as you connect to the CCB cluster.

As a result, when you connect to the CCB cluster in new instances of the Terminal application, you will only need to call the alias by name.

conda_activate_base

Furthermore, you should only call the alias once per Terminal application, as there is no benefit to activate the base environment multiple times per session.

The only exception being if you deactivate the base environment and wish to re-activate it. For instance, notice the (base) prefix appearing and disappearing from the promp as the environment is activated and de-activated in the example below:

conda_activate_base
conda deactivate
conda_activate_base