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The amplikyzer2 software is a pure Python program that uses the Numba package for speed improvements. This means that it runs on any operating system (OS) for which Python and the Numba package are available, including Windows, Mac OS X, and many Linux distributions.

We recommend using the Miniconda distribution of Python 3 (64-bit), which is available free of charge from Anaconda, Inc. This makes it easy to create a separate Python installation with all requirements for amplikyzer2 without disrupting your system Python. The following instructions assume that you are using the Miniconda (or Anaconda) distribution.

Installing Miniconda

Go to https://docs.conda.io/en/latest/miniconda.html and choose your operating system (Windows, Mac OS X, Linux), choose Python 3.*, and in some cases choose whether your OS is 32-bit or 64-bit. If you are not sure, try the 64 bit version first. If you get an error running the installer, you do not have a 64-bit OS; then use the 32-bit version. Download and run the installer.
If you are not using Python yet, it is recommended to check the option to modify the path to include conda. Otherwise, leave all options at their default values. (Of course, feel free to change them as you see fit for your system.)
Note that you do not need administrator privileges for installing Miniconda or Anaconda; you can just install it somewhere in your home directory.
In the end, it is important that the conda executable can be found in your PATH. Refer to the installation instructions for details on how to set your PATH environment variable if you do not let the installer do this.

Installing amplikyzer2 in a conda environment

Open a terminal window. Windows users can typically run the "Anaconda Prompt" from the "Anaconda3 (64-bit)" folder inside the start menu. The Anaconda Prompt automatically activates conda's root environment. Only when you are not using the Anaconda Prompt (e.g., on Windows, by simply running cmd.exe), you must activate the root environment with
```
conda activate
```
Update the conda package manager.
```
conda update conda
```
Install amplikyzer2 into a newly created environment.
- To install the GUI alongside amplikyzer2, as you typically would, run:
```
conda create --name amplikyzer2 -c genomeinformatics amplikyzer2gui
```
  By installing amplikyzer2gui you install amplikyzer2 as well as geniegui (which provides the GUI functionality) and an executable amplikyzer2gui with which you can launch the GUI directly.
- To only install amplikyzer2 itself without the GUI (not recommended), run:
```
conda create --name amplikyzer2 -c genomeinformatics amplikyzer2
```
Add our conda channel genomeinformatics to the just created amplikyzer2 environment.
```
conda activate amplikyzer2
conda config --env --append channels genomeinformatics
```
By adding the channel to the environment's configuration, you won't have to explicitly specify the channel when updating amplikyzer2 at a later point in time.

The installation is done. You can now start working with amplikyzer2.

Updating an existing version of amplikyzer2

If amplikyzer2 was already installed on your system as described above and you want to upgrade to a new version (because of new features or bugfixes), activate your conda environment and use conda to update amplikyzer2:

conda activate amplikyzer2  # activate the conda environment
conda update --all

This way you will also receive updates for the GUI and the underlying computational libraries. If you didn't add the genomeinformatics channel to the environment, you need to substitute the update command with conda update -c genomeinformatics --all.

Starting amplikyzer2

There are two versions, a GUI version (amplikyzer2gui) and a command line version (amplikyzer2). For each one there will be a corresponding executable in the environment's bin (Windows: Scripts) directory. Here is how to start either of them on Linux, MacOS X and Windows.

GUI version

You should run amplikyzer2 from a terminal inside an activated environment using the following commands:

conda activate amplikyzer2   # activate the conda environment
amplikyzer2gui               # run GUI via executable

Always remember to activate the amplikyzer2 environment before trying to start amplikyzer2gui via python -m.

On Windows, installing the amplikyzer2gui package should place shortcuts in the start menu as well as one the desktop, from which the GUI can be started. This may not work properly. Please use the instructions above then.

Command line version

As with the GUI version there is an executable amplikyzer2 in path/to/miniconda3/envs/amplikyzer2/bin (path\\to\\miniconda3\\envs\\amplikyzer2\\Scripts on Windows). You can either run it directly by path or through an activated environment using the following commands:

conda activate amplikyzer2               # activate the conda environment containing amplikyzer2
amplikyzer2 --help                       # show command help of the amplikyzer2 application
amplikyzer2 COMMAND --OPTIONS ARGUMENTS  # invoke amplikyzer2 with an appropriate command

Always remember to activate the amplikyzer2 environment before trying to start amplikyzer2 via python -m.

Next steps

You can now proceed to analyze a sample dataset, using the step-by-step explanations provided with our example, or go back to the overview page.