DOME is developed using python3 and R shiny package. The database is provided as a Tabix indexed (.tbi) TSV file along with the toolkit package for download.
The installation procedure is simplified by use of Conda environment. DOME package contains a conda environment file (.yml) which installs all the dependencies
directly for the user. The directory structure (files) within the DOME package are described below, followed by the installation instructions.
Pre-requisites required for installation of DOME
Users are required to download DOME package from the webpage. Approximately 2 GB of system space is required to store the package. The downloaded package needs to be extracted using "unzip" or "winrar" extractor, depending on the operating system used. The package contains the following contents:
DOME-main (root folder)
├── Manual (User Manual)
├── app.R (Rshiny App)
├── input_dome.txt (example: input file)
├── output (test output)
├── domeenv.yml (conda environment)
└── scripts (DOME algorithm and accesory scripts)
DOME requires reference databases, which need to be downloaded clicking the following link: DOME reference databases. Click on "Download" (select standard download), the file is 1.44 Gb in size. Place the downloaded "data.zip" in the root folder (dome) and unzip using 'unzip' command or any zip file extractor. DOME is now ready for installation.
The installation of the required packages is performed through Anaconda/Miniconda, which needs to be installed. With Conda installed, users can use the following commands in the Linux / Unix environment to install the required python packages.
DOME can be downloaded from this webpage. Unzip the downloaded .zip file using the following command:
Make sure that the complete 'unzipped' data directory is present in the dome home directory before proceeding with the further installation and running dome.
In the home directory of DOME (DOME-main), run the following command:
conda env create -f domeenv.yml