Installation

There are several ways to install the package.

Linux binary download

The easiest way to install Baysor on Linux is to download a binary from the release section (see Assets). There, you can use bin/baysor executable. For other platforms, "Install as a Julia package" is a recommended way. If you know how to reliably compile binaries for MacOS or Windows, please, let me know in issues or over email!

Install as a Julia package

If you need to install julia, juliaup is a recommended way. It's cross-platform and doesn't require admin privileges. TL;DR: curl -fsSL https://install.julialang.org | sh .

The current version of Baysor isn't compatible with Julia 1.11.

To install Julia 1.10, use the following command:

juliaup add 1.10
juliaup default 1.10

To install Baysor as a Julia package run the following command from your CLI (it requires gcc or clang installed):

julia -e 'using Pkg; Pkg.add(PackageSpec(url="https://github.com/kharchenkolab/Baysor.git")); Pkg.build()'

It will install all dependencies, compile the package and create an executable in ~/.julia/bin/baysor. This executable can be moved to any other place if you need it.

The same command can be used to update the package to the latest version.

Installing other versions

To install development version, use Pkg.add(PackageSpec(url="https://github.com/kharchenkolab/Baysor.git", rev="develop")):

julia -e 'using Pkg; Pkg.add(PackageSpec(url="https://github.com/kharchenkolab/Baysor.git", rev="develop")); Pkg.build()'

Other versions may be similarly installed by passing the version to the rev parameter (e.g., rev="v0.5.2").

Docker

Alternatively, you can use Docker. It contains executable baysor to run Baysor from CLI, as well as IJulia installation to use Baysor with Jupyter. The repo also has images for older versions.

docker run -it --rm vpetukhov/baysor:latest

Build by hands:

docker pull julia:latest
cd Baysor/docker
docker build .

You can find more info about dockers at Docker Cheat Sheet.