4.1. General Setup

If you don't want to configure the whole environment, we also offer a Docker-encapsulated version. For more details, see here

In this section, we will introduce how to setup the SnpHub. Basic knowledge about Linux, R and resequencing is required. Also, you need to have a server installed with shiny server. For more information, please read here.

Environment

To run the SnpHub, make sure the following software programs are already installed:

  • samtools (≥ v1.4)
  • bcftools (≥ v1.8)
  • seqkit
  • tabix (≥ v1.6)

Also, the following R packages are also prerequisites:

  • ggplot2
  • crayon
  • ggmap
  • dplyr
  • rjson
  • shiny
  • pegas
  • maps
  • vcfR
  • ape
  • DT

Demo

Two steps are needed to run on demo data set:

  • Using git to clone SnpHub to local.

    git clone https://github.com/esctrionsit/snphub

  • Using R to run on demo data set. (Or copy the SnpHub into your shiny-server app folder)

    R -e "shiny::runApp('./snphub', port=5000, host='0.0.0.0')"

Make sure that samtools, bcftools, seqkit and tabix are added to system PATH. Otherwise, tool application paths part in setup.conf is needed to change to fit.

Setup with your own data set

Fulfill config file

Basic config file is named setup.conf, fulfill it and then run command:

Rscript ./setup.R

Check configuration for more details about setup.conf.

Check file format for more details about required file formats.

If it is your first time to set up SnpHub, you need to delete advanced_config.R, and then rename advanced_config_O.R to advanced_config.R.

rm -f advanced_config.R && mv advanced_config_O.R advanced_config.R
Check the config file

Each time you reset/changed your configuration, use:

Rscript ./setup.R

to get the completeness checked and the raw data file pre-processed.