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Installation

Homebrew

For installing rastair locally on macOS and Linux, you can use homebrew:

brew tap bsblabludwig/rastair git@bitbucket.org:bsblabludwig/homebrew-rastair.git
brew install rastair

Docker

You can use the pre-built docker image in the usual way:

docker pull sbludwig/rastair:version-2.1.0

Building using Docker

You can also build Rastair using Docker. Ensure you have Docker installed and running on your system, then, clone the repo and build the image:

docker build -t rastair .

This image is based on the R base image and includes all necessary dependencies to also run the bundled R scripts.

Conda

conda create -n rastair_env -c conda-forge -c bioconda rastair=v2.1.0
conda activate rastair_env

Pre-built binaries

You can also download pre-built binaries for a number of platforms.

Linux

We provide a pre-built binary for Linux (x86):

This binary was built on Ubuntu 20.04 but should work on most recent distributions.

Info

While rastair itself is hard-linked and therefore independent of system libraries, this is unfortunately not yet the case for htslib. If your system uses a GLIBC older than 2.30, then you will have to compile from source.

Mac OSX

For Apple users, we provide both Apple Silicon and Intel binaries:

Building from source

Pre-requisites

To compile from source, you need a working Rust installation (version 1.88 or later). Rastair depends on rust-htslib, which currently requires a working clang library as well as cmake. On most systems, these are either already available or can be installed using a standard package manager:

First, clone the repo:

git clone git@bitbucket.org:bsblabludwig/bsblabludwig/rastair.git

Then follow the platform-specific instructions below.

Ubuntu

sudo apt install cmake

Fedora

sudo dnf install -y clang cmake

Mac OSX (Homebrew)

We assume that you have Xcode developer tools installed. In that case, you only need

brew install cmake

Compile

Finally, build the project using:

cargo xtask release

The binary will be located in target/release/rastair.

Tip

On some systems, you might get performance improvements by allowing the compiler to use platform-specific optimisations:

RUSTFLAGS="-C target-cpu=native" cargo xtask release