GATK4 Mutect2 error - SyntaxError - invalid syntax

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1

Hello,

When using GATK4 for a tumour only analysis on a local server, the tool errors out with a “SyntaxError: invalid syntax” error. I have tried different versions of GATK4 Mutect2 (4.1.7.0+galaxy1, 4.1.7.0+galaxy1+galaxy1, 4.1.70+galaxy0) and everytime GATK4 Mutect2 shows the same error. I am attaching a picture of the error here:

  File "/home/galaxyp_user/galaxyp/galaxy/database/dependencies/_conda/envs/mulled-v1-2d71e7294258e0d6557ab09c36c8336300de41c90ae1e21e30396938913db7d4/bin/gatk", line 150
    gatkArgs += ["--spark-master", sparkMaster]
              ^
SyntaxError: invalid syntax

I am running Galaxy 25.0.3.dev0.

This is similar to the error encountered in this topic (GATK4 Mutect2 Syntax Error). My error is occuring on a local Galaxy installation.

Thank you

Rao

2

Welcome @prao123

Thanks for sharing the error and other details. Yes, this legacy tool is a bit tricky to get configured correctly!

At UseGalaxy.org, the tool is now running with

Container ID → /cvmfs/singularity.galaxyproject.org/all/mulled-v2-a4c30dc1a2dfc3f31070c6a8acc1c627f7a22916:3255c0a2d99e5718efb40269116cc85ded9b1200-3

Please let us know if this helps! :slight_smile: