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cgab-ncc / FIREVAT

FInding REliable Variants without ArTifacts
MIT License
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Utilizing pandoc #5

Open vymao opened 4 years ago

vymao commented 4 years ago

Hi,

I noticed that FIREVAT depends on pandoc for creating figures, of which there does not seem to be an easy way to manually install. Is FIREVAT runnable from an R command line instance; if so, what version of R should we use, since pandocs doesn't seem available for R above R/3.2.5? Or is RStudio required?

khb7840 commented 4 years ago

I apologize for the late response. FIREVAT import "Rmarkdown" library (which converts .Rmd to html with "pandoc") during report generation step. If you have some problem with pandoc, I think you can skip report generation step with by setting "report = FALSE" when executing RunFIREVAT function.

FIREVAT script which can be executed as CLI is located at "scripts/firevat_run.R" in the repository. This version of script does not contain all of options in RunFIREVAT function. We will update soon.