VIRIDIC

VIRIDIC (Virus Intergenomic Distance Calculator) computes pairwise intergenomic distances/similarities amongst viral genomes. VIRIDIC is available at http://viridic.icbm.de as a web-service or a singularity package. In addition, the R language source code can be accessed from this repository.
If you use VIRIDIC, please cite: Moraru, C., Varsani, A., and Kropinski, A.M. (2020) VIRIDIC – a novel tool to calculate the intergenomic similarities of prokaryote-infecting viruses. Viruses 12(11). https://doi.org/10.3390/v12111268

This repository contains:

• the source code for the stand-alone VIRIDIC, written in R
• the source code for the shiny-app, which provides a graphical user interface for the standa-alone VIRIDIC

How to install VIRIDIC

• copy to your profile the content of the VIRIDIC folder

• create and activate the VIRIDIC conda env

  • use the yml file from /VIRIDIC/stand_alone/user-install/VIRIDIC.yml to create the VIRIDIC conda env
  • install the specific R libraries

  conda env create -f VIRIDIC.yml
  conda activate VIRIDIC

  Install R libraries from within R

  R  #this command starts R

  options(repos = c(CRAN = "https://cloud.r-project.org/"))
  
  install.packages("stringr")
  install.packages("magrittr")
  install.packages("dplyr")
  install.packages("tibble")
  install.packages("purrr")
  install.packages("tidyr")
  install.packages("ggplot2")
  install.packages("data.table")
  
  install.packages("DT")
  install.packages("shiny")
  install.packages("shinyjs")
  install.packages("shinyWidgets")
  install.packages("shinythemes")
  install.packages("seqinr")
  
  #install.packages("IRanges")
      if (!require("BiocManager", quietly = TRUE))
      install.packages("BiocManager")
      BiocManager::install("IRanges")
  
  install.packages("reshape2")
  install.packages("pheatmap")
  install.packages("fastcluster")
  install.packages("parallelDist")
  install.packages("furrr")
  install.packages("future")
  
  #install.packages("ComplexHeatmap")
      if (!require("BiocManager", quietly = TRUE))
      install.packages("BiocManager")
      BiocManager::install("ComplexHeatmap")

  How to run VIRIDIC shiny-app

• Open RStudio, create a new project for the folder VIRIDIC (directly in this folder there are the files of the shiny-app)

• open either ui.R or server.R files in RStudio, press button "Run App"

• this will start the VIRIDIC GUI, which then runs the VIRIDIC stand-alone code

• In addition, if you install the shiny-server, you can run VIRIDIC as an independent web-app.

How to run VIRIDIC stand-alone

• go to your folder with the VIRIDIC scripts
• use the command "Rscript 00_viridic_master.R [...options]"
• for options, see manual, either by running "Rscript 00_viridic_master.R help" or by checking the PDF file here: /VIRIDIC/stand_alone/download/viridic_manual_v1.1.pdf

# example of how to run one VIRIDIC analysis
    Rscript 00_viridic_master.R projdir=/home/cmoraru/TEST_CLM/testVIridic in=/home/cmoraru/TEST_CLM/Ebeline_rel.fna ncor=10