Question: How to set up SNPEff jars and tools on the Galaxy cloud instance?
1
gravatar for msprindzhuk
17 months ago by
msprindzhuk50
msprindzhuk50 wrote:

On running various SNPEff tools we have got:

Error: Unable to access jarfile /home/pcingola/tools/SnpSift.jar Error: Unable to access jarfile /Users/pablocingolani/snpEff/snpEff.jar

Java in $PATH as well as *.jars. How to fix that? What configuration file to change and how?

snpeff java jar • 426 views
ADD COMMENTlink written 17 months ago by msprindzhuk50
0
gravatar for msprindzhuk
17 months ago by
msprindzhuk50
msprindzhuk50 wrote:

question is solved, path was written in .xml files, thank you

ADD COMMENTlink written 17 months ago by msprindzhuk50

I have the same issue as you had. would you explain how to set up this path in details? Thank you

ADD REPLYlink written 12 weeks ago by hoky.kim20
1

My guess is that they were natively installing SnpEff reference data and they needed to reorganize the local data to match where the tool's XML is expecting to find this input.

The SnpEff tools have been updated recently so be sure you are using the latest version available in the Main ToolShed https://usegalaxy.org/toolshed.

ADD REPLYlink modified 11 weeks ago • written 11 weeks ago by Jennifer Hillman Jackson25k

thank you for your reply.

I needed to change snpEff.xml file to give a path to snpEff.jar file. This is also commented in snpEff.xml file.

ADD REPLYlink written 11 weeks ago by hoky.kim20
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