candiSNP
candiSNP is now an R package that you can run on your own computer.
You will need to install R and some packages to make it work. You will
also need a Java installation but that should already be present on
your machine.
Prerequisites
The SNPEff part of the process requires 2 Gb free memory in your
machine. You will therefore need a machine with greater than that to run
candiSNP. The process will not take more than 2 Gb, so at this time
the larger (e.g Human) databases will not run.
Installation
Install R
The R statistical programming language can be installed from one of
the CRAN mirrors listed here https://cran.r-project.org/mirrors.html.
You will need version 4.1.0 or later.
Install the candiSNP package
Once you have installed R, use the R console to install the development
version of candiSNP using the devtools package, install that first.
install.packages('devtools')Then you can install candiSNP
devtools::install_github("TeamMacLean/candiSNP")Installing genome annotations for SNPEff
candiSNP brings with it version 3.6 of SNPEff, but not any genome
annotations. To install the default genomes used in the original web
version of candiSNP you can use the install_default_genomes()
function.
At the R console, type
library("candiSNP")
install_default_genomes()This operation can take a few minutes, depending on your internet speed.
You should only need to do it once per candiSNP install, though.
Starting the app
Once the genomes are installed, you can proceed to start candiSNP as
follows.
app()Note that the app starts in a browser window. The R console remains
busy while the app is running. Use Ctrl-C or esc to quit the process
and get your console back.