Get Started

Installation

To install julia, please go to the offical Julia website. Please see platform specific instructions if you have trouble installing Julia.

To install the package, use the following command inside the Julia REPL (or IJulia Notebook):

Pkg.add("JWAS")

To load the JWAS package, use the following command inside the Julia REPL (or IJulia Notebook):

using JWAS

The command Pkg.add("JWAS") will add the registered official JWAS package and dependencies.

To use the latest/beta features under development, run Pkg.checkout("JWAS") to get the newest unofficial JWAS. Run Pkg.free("JWAS") to go back to the offical one.

IJulia notebook

If you prefer “reproducible research”, an interactive Jupyter notebook interface is available for Julia (and therefore JWAS). The Jupyter notebook is an open-source web application for creating and sharing documents that contain live code, equations, visualizations and explanatory text. To install IJulia, please go to IJulia.

Docker

• Install Docker from here for your platform.

• From a terminal (on Mac or Linux), run the command:

docker run -it --rm -p 8888:8888 qtlrocks/jwas-docker

This will start a Jupyter-IJulia Notebook server listening for HTTP connections on port 8888 with a randomly generated authentication token. Examples for JWAS can be accessed from the notebook: JWAS_notebooks/index.ipynb.

The directories and files created within the Docker container will be lost when the container is stopped. To save your work on the host machine, a directory on the host machine can be mounted as a folder in the container with the command:

docker run -it --rm -p 8888:8888 -v path_to_folder_on_host:/home/jovyan/folder_in_container qtlrocks/jwas-docker

where path_to_folder_on_host is the path to the folder that you want to have access to from within the container, and folder_in_container is the name of the folder in the container. For example, the Docker command

docker run -it --rm -p 8888:8888 -v /Users/rohan:/home/jovyan/rohan qtlrocks/jwas-docker

creates a Docker container with the folder rohan with the contents of /Users/rohan of the host machine. Files and directories that are in the folder /home/jovyan/rohan will not be lost when the container is stopped.

Standalone application

Access documentation

To show the basic information (README file) of JWAS in REPL or IJulia notebook using ?JWAS and press enter.

For help on a specific function, type ? followed by its name, e.g. ?runMCMC and press enter in REPL or IJulia notebook.

The full documentation is available here.

Run your analysis

There are several ways to run your analysis.

(1) The easiest way to run analysis in Julia is by starting an interactive session (REPL) by double-clicking the Julia executable or running julia from the command line (e.g., terminal) as

julia> 1+2
3

julia> 3*4
12

To evaluate code written in a file script.jl in REPL, write and run

julia> include("script.jl").

To exit the interactive session, type ^D – the control key together with the d key or type quit().

(2) To run code in a file non-interactively from the command line (e.g.,termial), you can give it as the first argument to the julia command:

julia script.jl

If you want to pass arguments to your script, run it as

julia script.jl arg1 arg2

where arguments arg1 and arg2 are passed to your script as ARGS[1] and ARGS[2] of type String. Please see julia docs for more options.

(3) To run code in IJulia notebook, please see IJulia.

(4) To run code in IJulia notebook via Docker, please see Jupyter-IJulia notebooks via Docker.