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bioinfoUGR / sRNAtoolbox

small RNA analysis programs: standalone jar files (sRNAbench, sRNAde, etc), manuals and Docker image
MIT License
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Unable to get graphical display #5

Open pmcsa opened 2 years ago

pmcsa commented 2 years ago

Hello all,

I'm trying to use the sRNAtoolbox, more specifically, the sRNAbench.jar in standalone. The command that I am running is the following:

java -jar sRNAbench.jar input=SRR8889097.fastq.gz output=sRNAtoolbox_out dbPath=/path-to/opt/sRNAtoolboxDB microRNA=ssc miRdb=1 graphics=true libs=/path-to-refgen/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa

Even though I specify "graphics=true", I get an empty "graphs" folder. I suspect it is because I don't have any R script in the sRNAtoolboxDB and I cannot seem to find them anywhere. Can anyone help me with that?

Many thanks!

sert23 commented 2 years ago

Hi @pmcsa , sorry for the inconvenience. I'm not sure if providing that folder will actually generate the graphs (as dependencies, etc should be installed too). But I attach it to this message so you can try.

r.zip

let us know if that solved your issue

Best Ernesto