Software requirements and installation

There are two components to an Autocycler installation:

1. Autocycler itself
2. the long-read assemblers needed to produce Autocycler's input assemblies

The first part (Autocycler itself) should be easy! Autocycler runs on macOS and Linux, and it is a standalone tool which does not rely on other software to run.

The second part (long-read assemblers) can be trickier, since these are external tools. While some assemblers can be installed on macOS, Linux will generally be a better platform for these tools.

Installing Autocycler

From pre-built binaries

Autocycler compiles to a single executable binary called autocycler.

Each release of Autocycler contains pre-built binaries for common operating systems, so most users can download the appropriate binary for their system and put the autocycler file in a directory in their PATH variable, e.g. /usr/local/bin/ or ~/.local/bin/.

If you're installing Autocycler to a conda environment (see notes below), activate the environment and then copy the Autocycler binary to the "$CONDA_PREFIX"/bin/ directory.

If you can successfully run autocycler --help, then you should be good to go.

Alternatively, you can skip installation and just run Autocycler from wherever the executable file is, like this: /some/path/to/autocycler --help.

Note for macOS users: When trying to run Autocycler, you might encounter a message saying "autocycler" cannot be opened because it is from an unidentified developer. If so, go to System Settings, then Privacy & Security, and under "autocycler" was blocked from use because it is not from an identified developer, click 'Allow Anyway'.

From source

There are a few reasons why you might want to build Autocycler from its source code:

• The pre-built binaries are incompatible with your hardware or OS.
• You want a version of Autocycler that doesn't correspond to a release (e.g. the latest commit on the main branch).
• You want to modify the source code.

If any of these apply to you, install Rust if you don't already have it. Then clone and build Autocycler like this:

git clone https://github.com/rrwick/Autocycler.git
cd Autocycler
cargo build --release

You'll find the freshly built executable in target/release/autocycler, which you can then move to an appropriate location that's in your PATH variable.

Installing long-read assemblers

Conda environment

The Autocycler repo contains a scripts directory with a conda environment file for installing some commonly-used long-read assemblers: Canu, Flye, LJA, metaMDBG, miniasm+Minipolish, NECAT, NextDenovo+NextPolish, Raven and Redbean.

To create an environment with these assemblers, run this from the scripts directory:

conda env create --file environment.yml --name autocycler

Notes:

• Depending on your platform, not all of these assemblers may be available, in which case you might encounter a PackagesNotFoundError error or something similar. If this happens, you can delete (or comment out) the relevant lines of environment.yml and try again.
• Autocycler does not require any specific assemblers to work, just a range of different assemblers – see the Generating input assemblies page for more information.
• You can use mamba instead of conda in the installation command if you have mamba installed, and it will probably be faster.

Helper scripts

The scripts directory also contains some Python and Bash scripts to help with generating input assemblies and genome size estimation.

To copy the helper scripts into your conda environment, first activate your environment and then run this command from the scripts directory:

cp *.py *.sh "$CONDA_PREFIX"/bin