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'No genomes installed!' error from getREF #58

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MarcoDiS opened this issue Nov 10, 2020 · 0 comments
Open

'No genomes installed!' error from getREF #58

MarcoDiS opened this issue Nov 10, 2020 · 0 comments

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@MarcoDiS
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MarcoDiS commented Nov 10, 2020

I was trying to use the getPlotSetArray() function, but I got the error 'No genomes installed!' from the getREF function. I digged into the problem and it turns out that in the latest version of the BSgenome package the output of the function BSgenome::installed.genomes(splitNameParts=TRUE) changed from:
pkgname organism provider provider_version masked
1 BSgenome.Hsapiens.UCSC.hg38 Hsapiens UCSC hg38 FALSE

to
pkgname organism provider genome masked
1 BSgenome.Hsapiens.UCSC.hg38 Hsapiens UCSC hg38 FALSE

To fix the error I added at line 94 of the helper_functions.R script the new line:
if( !length(GENOMES) ) GENOMES <- BSgenome::installed.genomes(splitNameParts=TRUE)$genome

Hope this helps!

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