Download and Run

Download the Source

You can download the source from GitHub, using this link or cloning the repository with the following command in your terminal. This requires git installed on your machine.

git clone https://github.com/danilexn/chromo
cd chromo

From R or RStudio

Prerequisites

The following must be installed in your local machine:

• R (we recommend using RStudio). You can find installation instructions for RStudio here
• libglpk-dev (for Linux; you will be asked for root password)

sudo apt-get update -y; sudo apt-get install -y libglpk-dev

More specifically, ChroMo depends on some R packages that must be previously installed. To make sure everything is ready, you can run the following command (inside a R console or in RStudio):

chromo.packages <- c("shiny", "shinycssloaders", "promises", "future", "ipc", "forecast", "dplyr", "ggplot2", "dplR", "lmtest", "purrr", "tidyr", "reshape2", "tseries", "segclust2d", "segmenTier", "mclust", "lattice", "TTR", "egg", "readxl", "RCurl", "shinythemes", "ggpubr", "htmlwidgets", "plotly", "rapportools", "tie", "pcalg", "VLTimeCausality", "network", "sna", "networkD3", "igraph", "GGally", "PerformanceAnalytics")

install.packages(chromo.packages)

Once all packages have been installed, you can run ChroMo on R, with the following command on your terminal:

cd chromo/app # if not in ChroMo directory
Rscript app.R

You will be displayed something like this

2 files sourced from folder "plots"
5 files sourced from folder "analysis"
3 files sourced from folder "calculators"

Listening on http://127.0.0.1:5170

This means that you can open a browser, and navigate to http://127.0.0.1:5170 to open the local instance of ChroMo.

Alternativelly, you can open the file app.R inside the chromo/app directory using RStudio, and click on Run App. This button is located on the upper-right corner of the source code layout.

Using Docker

Prerequisites

You will need the following:

• Docker. Please, find here the install instructions

Optionally, you can also use:

• ShinyProxy, if you are going to deploy a multi-user instance on your own server. Please, find here the install instructions

Run with Docker only

First, you will need to download the Docker image

docker pull docker.pkg.github.com/danilexn/chromo/chromo:latest

Then, you can change the name of the image to something more descriptive

docker tag docker.pkg.github.com/danilexn/chromo/chromo chromo-local

You will need to create a bookmarks directory to enable local storage of analyses with the bookmarking functionality. For example:

mkdir /home/<user>/bookmarks
chmod -R 0777 /home/<user>/bookmarks

Just replace <user> with your username. Also, you can specify a different directory; be aware that you will need to change the corresponding argument to chmod (above).

Finally, you can run ChroMo with Docker

docker run -v /home/<user>/bookmarks:/home/chromo/app/shiny_bookmarks -p 3838:3838 chromo-local

Just replace <user> with your username, or the whole first path by the actual route of the local bookmarks directory. Moreover, you can change any of the settings in the command above, e.g., regarding ports or memory and CPU allocation. Check Docker's official reference guide for more information.

You can now open localhost:3838 on your favourite web browser, and start using ChroMo.

Configure ShinyProxy

ShinyProxy will allow to run multiple instances of ChroMo on the same server, by taking advantage of containerization through Docker. We provide our own configuration profiles on ChroMo's main GitHub repository. Please, find here the whole reference guide to ShinyProxy for more advanced configuration settings.

1. First, you will need to download the Docker image following the steps above.
2. Clone ChroMo's repo using the steps above.
3. Copy ShinyProxy's executable and configuration files into the corresponding local directory

cp net/shinyproxy/shinyproxy.jar /opt/shinyproxy/shinyproxy.jar
cp net/shinyproxy/application.yml /etc/shinyproxy/application.yml

4. Our configuration file, application.yml, will make ShinyProxy expect three types of instance (ChroMo S, M and L). You can either change this configuration file with your own image names, or create the three expected images:

docker tag docker.pkg.github.com/danilexn/chromo/chromo danilexn/chromo-s:latest
docker tag docker.pkg.github.com/danilexn/chromo/chromo danilexn/chromo-m:latest
docker tag docker.pkg.github.com/danilexn/chromo/chromo danilexn/chromo-l:latest

5. Restart ShinyProxy, making sure that all Docker containers have been stopped. Otherwise, there may be conflicts creating new containers after the restart.

sudo service shinyproxy stop
docker stop $(docker ps -q)
sudo service shinyproxy start

The ShinyProxy server should be reachable at localhost:8080 on a web browser.