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 for these tools.

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) via conda

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

To create a conda environment with Autocycler and these assemblers, run this from the scripts directory:

conda env create --file environment.yml --name autocycler 
conda activate autocycler
cp *.py *.sh "$CONDA_PREFIX"/bin  # copy assembly helper scripts into conda env
plassembler download -d "$CONDA_PREFIX"/plassembler_db  # download plassembler_db

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.