Installation for personal use

SCI-VCF can be installed locally in multiple ways!

Online access

Important: The online version of SCI-VCF is on shinyapps.io, currently hosted on Amazon’s Web Services (AWS) infrastructure in the US-east-1 region. The infrastructure used is not the HIPAA-compliant stack, and users must take care to upload only anonymized and appropriate data. To work with sensitive data, we recommend a local installation of SCI-VCF.

Step 1: Open the SCI-VCF website.

Note: The online version of SCI-VCF comes with upload size limitations. To get the full functionalities of SCI-VCF, use a local/server installation of the tool.

RStudio based installation

Prerequisites

Procedure

Step 1: Get the SCI-VCF repository from GitHub.

You can download the zipped version of the repo at this link

github_download_image

Step 2: Extract the files on your computer.

This will create a folder in your computer called SCI-VCF-main. Open that folder.

Step 3: Launch SCI-VCF

Open the folder named R. Open global.R with RStudio and click the Run App button.

rstudio_runapp_image

Note: The first time you launch SCI-VCF by clicking the Run App button, some dependencies will be downloaded. Kindly wait till then. You need to be connected to the internet and might need to give authorization if required. Once the dependencies are installed, SCI-VCF can be used offline thereafter.


Conda-based installation

Prerequisites

  • Conda (link)
  • Command Line Interface

Procedure

Step 1: Get the SCI-VCF repository from GitHub

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

Step 2: Open the SCI-VCF directory

cd SCI-VCF

Step 3: Create the conda environment with all required dependencies 

conda env create -f conda/SCI-VCF_conda_env.yaml

Step 4: Activate the conda environment created

conda activate SCI-VCF

Step 5: Open global.R with R

Rscript R/global.R

The following output will be printed

conda_installation

Step 6: Open SCI-VCF in a browser

Copy the IP address at the end of the CLI output from Step 5. Paste it in a browser search tab and load the same. SCI-VCF will be launched.

Note: For conda-based installation in Windows OS, we recommend using the Windows Subsystem for Linux. More information is available in the FAQ section.

Docker-based installation

Prerequisites

  • Docker (link).
  • Web Browser
  • Sudo privileges

Step 1: Get the SCI-VCF image from Docker Hub and run it

sudo docker run -it --rm -p 3000:3000 venkatk89/sci-vcf

Step 2: Open SCI-VCF via browser using the address below:

http://0.0.0.0:3000/

Note: The docker command in step 1 is to run the container interactively, which makes SCI-VCF inactive when the terminal is exited. Docker containers can also be run detached from the terminal as a backend job. When the docker image is run this way, SCI-VCF will always stay active at the link mentioned in Step 2. More information is available in the FAQ section.