EpiAnnotator Installation

Yassen Assenov

2017-11-04

This document describes how to make a local installation of EpiAnnotator.

Prerequisites

EpiAnnotator is implemented as an R package and, therefore, you first need to make sure you have a recent version of R installed on your system. For more information on how to install R, please follow the instructions provided on the R download page. Also, make sure that you have permissions to update existing R packages, and to install new ones.

Step 1: Installing the R Package

In order to install the most recent version of EpiAnnotator, you just need to start a new R session and to execute the following command:

source("http://computational-epigenomics.com/downloads/EpiAnnotator.R")

This command downloads a dedicated R script from the Computational Epigenomics website that installs EpiAnnotator along with its dependencies.

Step 2: Download Databanks

In order to run EpiAnnotator locally, you need at least one databank containing annotations to work on. One databanks is a large organized collection of files, it resides in its dedicated directory and can take up several Gigabytes of disk space. Copies of the latest releases of EpiAnnotator databanks are hosted on Mega.

First, create two new empty directories: one to contain the databanks, and another one to store enrichment analysis results. Then, download one or more of the archive files listed in the table below and unpack them in the newly created directory for databanks.

Databank Annotations Approximate size (GB) Download link
EpiAnnotator_hg38 2066 3.4 tar file
LOLA_Core_hg38 2969 0.3 tar file
LOLA_Extended_hg38 1239 1.4 tar file
EpiAnnotator_hg19 318 0.8 tar file
LOLA_Core_hg19 3012 0.4 tar file
LOLA_Extended_hg19 1239 1.4 tar file
EpiAnnotator_mm10 79 0.9 tar file
EpiAnnotator_mm9 2 0.1 tar file

As an example, if you create the following new directories on your MacOS system:

/Users/Steve/EpiAnnotator/Databanks

/Users/Steve/EpiAnnotator/Analyses

then download and unpack the EpiAnnotator_hg38 databank, it will create the following directory:

/Users/Steve/EpiAnnotator/Databanks/EpiAnnotator_hg38

Step 3: The Shiny App

The interface of EpiAnnotator is implemented as a Shiny app. Following the example from above, you can launch EpiAnnotator’s interface by starting an R session and typing the following commands:

suppressPackageStartupMessages(library(EpiAnnotator))
epi.shiny.analysis("/Users/Steve/EpiAnnotator/Databanks", "/Users/Steve/EpiAnnotator/Analyses")

The second command downloads the latest release of the Shiny app from the Computational Epigenomics website and starts it.