Deploy SCI-VCF for communal use

SCI-VCF can be deployed using Shiny-Server for communal use. Sudo access might be required for this purpose. Such a deployment would make SCI-VCF accessible to everyone connected to the institute's intranet.

Step 1: Install R

sudo apt-get install r-base

SCI-VCF is compatible with R version >= 4.2. For installation guidelines, the documentation can be followed.

Step 2: Install dependencies of SCI-VCF

sudo su - -c "R -e \"install.packages('shiny', repos='https://cran.rstudio.com/')\""

sudo su - -c "R -e \"install.packages('rmarkdown', repos='https://cran.rstudio.com/')\""

sudo su - -c "R -e \"install.packages('vcfR', repos='https://cran.rstudio.com/')\""

sudo su - -c "R -e \"install.packages('here', repos='https://cran.rstudio.com/')\""

sudo su - -c "R -e \"install.packages('ggplot2', repos='https://cran.rstudio.com/')\""

sudo su - -c "R -e \"install.packages('scales', repos='https://cran.rstudio.com/')\""

sudo su - -c "R -e \"install.packages('eulerr', repos='https://cran.rstudio.com/')\""

sudo su - -c "R -e \"install.packages('dplyr', repos='https://cran.rstudio.com/')\""

sudo su - -c "R -e \"install.packages('tidyr', repos='https://cran.rstudio.com/')\""

sudo su - -c "R -e \"install.packages('reshape2', repos='https://cran.rstudio.com/')\""

sudo su - -c "R -e \"install.packages('shiny', repos='https://cran.rstudio.com/')\""

sudo su - -c "R -e \"install.packages('shinycustomloader', repos='https://cran.rstudio.com/')\""

sudo su - -c "R -e \"install.packages('colourpicker', repos='https://cran.rstudio.com/')\""

sudo su - -c "R -e \"install.packages('plotly', repos='https://cran.rstudio.com/')\""

sudo su - -c "R -e \"install.packages('htmltools', repos='https://cran.rstudio.com/')\""

sudo su - -c "R -e \"install.packages('reactable', repos='https://cran.rstudio.com/')\""

Step 3: Install shiny-server

Get gdebi to install .deb files

sudo apt-get install gdebi-core

Get the .deb file for shiny-server

wget https://download3.rstudio.org/ubuntu-18.04/x86_64/shiny-server-1.5.20.1002-amd64.deb

Install shiny-server with gdebi

sudo gdebi shiny-server-1.5.20.1002-amd64.deb

Check the status of the shiny-server

systemctl status shiny-server.service

Verify that Shiny has been installed correctly

Attempt a connection from a different machine on the same network by visiting: your.server.ip_address:3838

Step 4: Get SCI-VCF from GitHub and alter it

Go to the shiny-server location

cd /srv/shiny-server/ 

Get SCI-VCF

sudo git clone https://github.com/HimanshuLab/SCI-VCF

cd SCI-VCF

Alter the file structure

sudo rm Dockerfile
sudo rm README.md
sudo rm -r conda/

Move all R files to the main directory

sudo mv R/* ./

Delete the empty R directory

sudo rm -r R

Change the global.R file

sudo vim global.R

Change relative paths of all utilities.

Change the below code block

source(here("./R/summarize_vcf.R"))
source(here("./R/compare_vcf.R"))
source(here("./R/plot_vcf.R"))
source(here("./R/server.R"))
source(here("./R/ui.R"))

to

source(here("./summarize_vcf.R"))
source(here("./compare_vcf.R"))
source(here("./plot_vcf.R"))
source(here("./server.R"))
source(here("./ui.R"))

Step 5: Check the deployment

SCI-VCF will now be available at your.server.ip_address:3838/SCI-VCF/

Note: For better user experience, the hyperlinks in the tool can also be made to open in a new browser tab