Software requirements and installation - rrwick/Autocycler GitHub Wiki

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.

Installing just 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/.

Autocycler is also in bioconda, so you can install it with conda install autocycler.

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 everything (Autocycler + long-read assemblers)

There's no one-size-fits-all method for installing Autocycler along with all the long-read assemblers it supports – different users and systems have different needs. That's why this repo doesn't prescribe a single installation approach. Instead, the pipelines directory provides several options for creating a working environment. If you have your own setup that works well, contributions to the pipelines directory are welcome via pull request!

Available options: