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Question: How to set up SNPEff jars and tools on the Galaxy cloud instance?
1
gravatar for msprindzhuk
21 months ago by
msprindzhuk • 50
msprindzhuk • 50 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 • 550 views
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written 21 months ago by msprindzhuk • 50
0
gravatar for msprindzhuk
21 months ago by
msprindzhuk • 50
msprindzhuk • 50 wrote:

question is solved, path was written in .xml files, thank you
ADD COMMENT • link written 21 months ago by msprindzhuk • 50

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

ADD REPLY • link written 6 months ago by hoky.kim • 20
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 REPLY • link modified 6 months ago • written 6 months ago by Jennifer Hillman Jackson ♦ 25k

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 REPLY • link written 6 months ago by hoky.kim • 20
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