Installation for personal use

SCI-VCF can be installed locally, in multiple ways!

Online access

Step 1: Open the SCI-VCF website.

Note: 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 in your computer.

This will create a foler in you 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 from the R directory in RStudio

rstudio R/global.R

Step 5: Launch SCI-VCF by clicking the Run App button.

Note: For conda-based installation in Windoas 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 privelleges

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.