3.1.5. Notes#

The command-line version (apt)#

You can use the apt package manager to install software from the command-line.

Searching for software#

Open a terminal to perform a search for matching packages in the repositories.

For example, here is a search for pymol

apt search pymol


You do not need to include sudo here.

This will output matching results from repositories, if any:

p   pymol           - Molecular Graphics System
p   pymol-data      - data files for PyMOL
p   python3-pymol   - Molecular Graphics System (Python 3 module

Once you have identified the correct package name — in this case, it is pymol you can proceed towards installing the package.

Installing a package#

You can install a package using the following command:

sudo apt install pymol


You need to include sudo here.

Also, in the commands below, you will be asked to enter your password.

You will also need to confirm if you would like to continue with the changes. Type y and then press the ENTER key to proceed.

[sudo] password for user:
Reading package lists... Done
Building dependency tree
Reading state information... Done
The following additional packages will be installed:
  pymol-data python3-pymol
The following NEW packages will be installed:
  pymol pymol-data python3-pymol
0 upgraded, 3 newly installed, 0 to remove and
4 not upgraded.
Need to get 0 B/5,192 kB of archives.
After this operation, 19.8 MB of additional disk
space will be used.
Do you want to continue? [Y/n] y

The package will now be installed.

Removing an installed package#

To remove an installed package, use the command:

sudo apt remove pymol

The command above does not remove dependent packages. You can remove them using:

sudo apt autoremove

Updating packages#

To update all installed packages, you can use these commands:

sudo apt update
sudo apt upgrade

To update a specific package — if an update is available, you can simply use apt install again:

sudo apt install package_name

Why is this a quick and easy method?#

You can use a graphical user interface (Software Manager) or the command-line (apt) to install software available in Linux package repositories.

Software installed in this manner will also be kept updated along with the rest of the system.

Additional software repositories#

It takes some time for newer versions of software to become available in distribution repositories.

If your software of interest is not available or if you need a more recent version of the software, you could try installing them from these additional sources:


Software installed using these methods, will also need to be kept updated manually.