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bugfix: fix the issue with the custom files not working properly #81

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merged 1 commit into from
Aug 10, 2024
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bugfix: fix the issue with the custom files not working properly #81

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2 changes: 1 addition & 1 deletion DESCRIPTION
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
Package: igvShiny
Title: igvShiny: a wrapper of Integrative Genomics Viewer (IGV - an interactive
tool for visualization and exploration integrated genomic data)
Version: 1.0.0
Version: 1.0.1
Date: 2024-08-10
Authors@R: c(
person("Paul","Shannon", role = c("aut"),
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3 changes: 3 additions & 0 deletions NEWS.md
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@@ -1,3 +1,6 @@
## igvShiny 1.0.1 - 2024-08-10
* fix issue with custom files not working properly

## igvShiny 1.0.0 - 2024-08-10
* sync with Bioconductor (3_19 release)

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6 changes: 3 additions & 3 deletions R/igvShiny.R
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Expand Up @@ -84,13 +84,13 @@ igvShiny <- function(genomeOptions,
destination <- file.path(directory.name, basename(gff3.file))
file.copy(gff3.file, destination, overwrite = TRUE)
genomeOptions[["annotation"]] <-
file.path(directory.name, basename(gff3.file))
file.path(basename(directory.name), basename(gff3.file))
}
# now that they have been copied, store the new paths
genomeOptions[["fasta"]] <-
file.path(directory.name, basename(fasta.file))
file.path(basename(directory.name), basename(fasta.file))
genomeOptions[["fastaIndex"]] <-
file.path(directory.name, basename(fasta.indexFile))
file.path(basename(directory.name), basename(fasta.indexFile))
} # if custom genome, local files

state[["requestedHeight"]] <- height
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Binary file removed inst/demos/customGenomes/.customGenome-localFiles-sars.R.swp
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9 changes: 4 additions & 5 deletions inst/demos/customGenomes/customGenome-localFiles-sars.R
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Expand Up @@ -11,12 +11,13 @@ annotation.file <- file.path(data.directory, "Sars_cov_2.ASM985889v3.101.gff3")

title <- "SARS-CoV-2"
genomeOptions <- parseAndValidateGenomeSpec(genomeName=title,
initialLocus="all",
initialLocus= NA,
stockGenome=FALSE,
dataMode="localFiles",
fasta=fasta.file,
fastaIndex=fastaIndex.file,
genomeAnnotation=annotation.file)
genomeAnnotation=annotation.file
)
#----------------------------------------------------------------------------------------------------
ui = shinyUI(fluidPage(
igvShinyOutput('igvShiny_0'),
Expand All @@ -26,9 +27,7 @@ server = function(input, output, session) {

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

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