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.
To run the SnpHub, make sure the following software programs are already installed:
- samtools (≥ v1.4)
- bcftools (≥ v1.8)
- tabix (≥ v1.6)
Also, the following R packages are also prerequisites:
Two steps are needed to run on demo data set:
gitto clone SnpHub to local.
git clone https://github.com/esctrionsit/snphub
Rto 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
tabix are added to system PATH. Otherwise,
tool application paths part in
setup.conf is needed to change to fit.
Basic config file is named
setup.conf, fulfill it and then run command:
Check configuration for more details about
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
rm -f advanced_config.R && mv advanced_config_O.R advanced_config.R
Each time you reset/changed your configuration, use:
to get the completeness checked and the raw data file pre-processed.