unable to start examples of igvShinyDemo-customGenome-localFiles.R

[tboonf]

Hi - I have been trying to load my own files using igvShiny but it hasnt been working. So I tried a few examples igvShinyDemo-customGenome-http.R, igvShinyDemo-customGenome-localFiles.R and none of them work. Its works when files are sourced from https but not for files uploaded locally.

_____For example the script that comes with igvShiny doesnt work even though the fasta, fai and gff3 actually exist in the right directory---- library(shiny) library(igvShiny) library(htmlwidgets)

library(biomaRt)

#---------------------------------------------------------------------------------------------------- data.directory <- system.file(package="igvShiny", "extdata") fasta.file <- file.path(data.directory, "ribosomal-RNA-gene.fasta") fastaIndex.file <- file.path(data.directory, "ribosomal-RNA-gene.fasta.fai") annotation.file <- file.path(data.directory, "ribosomal-RNA-gene.gff3")

genomeOptions <- parseAndValidateGenomeSpec(genomeName="ribo local", initialLocus="U13369.1:7,276-8,225", stockGenome=FALSE, dataMode="localFiles", fasta=fasta.file, fastaIndex=fastaIndex.file, genomeAnnotation=annotation.file)

#---------------------------------------------------------------------------------------------------- ui = shinyUI(fluidPage( igvShinyOutput('igvShiny_0'), )) #---------------------------------------------------------------------------------------------------- server = function(input, output, session) {

output$igvShiny_0 <- renderIgvShiny({ cat("--- starting renderIgvShiny\n"); x <- igvShiny(genomeOptions, displayMode="SQUISHED", ) cat("--- ending renderIgvShiny\n"); return(x) })

} # server #---------------------------------------------------------------------------------------------------- if(grepl("hagfish", Sys.info()[["nodename"]]) & !interactive()){ runApp(shinyApp(ui, server), port=6867) } else { shinyApp(ui, server) }