Creation of a Shiny server to develop population genetic tool ocurred to us while working on [poppr] (https://github.com/poppr/poppr) on the winter of 2013.
The goals of the Genotype-ID are
- To create an easy framework for the reconstruction and identification on SSR data
- To use [poppr] (https://github.com/poppr/poppr) in a highly efficient way, in order to create web-apps for biologists/researchers everywhere
- To generate a genotyping webpage for species of Phytopthora
- Phytophthora ramorum
Genotype-ID is based on R, it uses:
- The latest R version (Version 2.15.3 is currently supported)
- [poppr] (https://github.com/poppr/poppr) package and its dependencies. Note: Right now, poppr must be in bleeding edge version for the NJ to work. In this case, refer to poppr manual to install it.
- [Shiny server] (https://github.com/rstudio/shiny-server) and its dependencies
After installing the requirements, be sure that you have a folder named shiny-server on /var/. Download the files into /var/shiny-server/ using git pull:
$ git pull https://github.com/Tabima/Genotype-ID/
After downloading the files, start the shiny-server
$ sudo shiny-server &
And go to your preferred browser (Genotype-ID is known to have issues with Internet Explorer, so we recommend using Google Chrome or, better yet, Firefox) and go to the server port address:
http://localhost:3838/
The browser will show you a link to a folder called "Genotype-ID/", if you click on it, the application will deploy on shiny server and voila! there is your web-app.