Authors
DOIs	Repo: Data:

All analysis code for this project is written in julia. In order to run it, follow the instructions below.

First, download the appropriate binaries for your system from the julia website and follow the installation instructions found there. Code has been tested against julia v1.6.

Once completed, you should be able to execute julia from the command prompt to open the julia REPL.

$ julia
               _
   _       _ _(_)_     |  Documentation: https://docs.julialang.org
  (_)     | (_) (_)    |
   _ _   _| |_  __ _   |  Type "?" for help, "]?" for Pkg help.
  | | | | | | |/ _` |  |
  | | |_| | | | (_| |  |  Version 1.6.0 (2021-03-24)
 _/ |\__'_|_|_|\__'_|  |
|__/                   |

julia>

Type exit() and then enter from the julia REPL to get back to your terminal's command prompt.

If you have git installed, the easiest way to obtain this code is to clone the repository.

$ git clone https://github.com/Klepac-Ceraj-Lab/ResonanceMicrobiome.git
Cloning into 'ResonanceMicrobiome'...
remote: Enumerating objects: 289, done.
remote: Counting objects: 100% (289/289), done.
remote: Compressing objects: 100% (175/175), done.
remote: Total 289 (delta 184), reused 213 (delta 109), pack-reused 0
Receiving objects: 100% (289/289), 9.01 MiB | 9.26 MiB/s, done.
Resolving deltas: 100% (184/184), done.
$ cd ResoncanceMicrobiome
$ git checkout v0.5.0

The final command checks out the version of the repository from the initial submission. You may also use the main branch, but this is not guaranteed to work. That said, if you find any problems with either the release or with the main branch, please open an issue and I will attempt to solve it as soon as possible.

Alternatively, the current release of these analysis notebooks can be downloaded from the releases page. Simply download and unpack the archive file.

TODO: add correct link once release is made

$ curl -O https://github.com/Klepac-Ceraj-Lab/ResonanceMicrobiome/archive/refs/tags/v0.5.0.tar.gz
$ cd ResonanceMicrobiome

The root directory has two files that enable easy replication of the julia project environment and its dependencies, Project.toml and Manifest.toml. To use them, start a julia REPL, activate the environment, and instantiate:

$ julia
               _
   _       _ _(_)_     |  Documentation: https://docs.julialang.org
  (_)     | (_) (_)    |
   _ _   _| |_  __ _   |  Type "?" for help, "]?" for Pkg help.
  | | | | | | |/ _` |  |
  | | |_| | | | (_| |  |  Version 1.6.0 (2021-03-24)
 _/ |\__'_|_|_|\__'_|  |
|__/                   |

julia> using Pkg

julia> Pkg.activate(".")
Activating environment at `~/repos/lab/testing/ResonanceMicrobiome/Project.toml`

julia> Pkg.instantiate()

Then, take a look at the files in the notebooks/ folder to get started. The .jl files are julia files, written in Literate.jl style. are meant to be viewed in order. All code is executed with the working directory set to the root of this repository.