Question: GATK3 Wrapper Error
gravatar for BAB Lab
2.6 years ago by
BAB Lab40
University of Oregon
BAB Lab40 wrote:

Hi everyone, first time poster here, sorry if this is the wrong place for this. I just recently installed the latest stable checkout of Galaxy and am working on getting my tools up and running, ran into a bit of a roadblock. I installed the GATK v.3 wrapper from avowinkel (revision b80ff7f43ad1). Jobs fail with the following output:

Traceback (most recent call last): File "/home/galaxy/galaxy/lib/galaxy/jobs/runners/", line 166, in prepare_job job_wrapper.prepare() File "/home/galaxy/galaxy/lib/galaxy/jobs/", line 889, in prepare self.command_line, self.extra_filenames, self.environment_variables = File "/home/galaxy/galaxy/lib/galaxy/tools/", line 442, in build raise e TypeError: unsupported operand type(s) for +: 'SelectToolParameterWrapper' and 'str'

I've tried digging through the wrappers to figure out where things are going off the rails, but I just don't have the coding ability to track this thing down. I tried starting with the .xml wrappers themselves, and also tried backtracking from the file referenced in the error. Has anyone else run into this particular issue?

software error galaxy • 1.0k views
ADD COMMENTlink modified 2.4 years ago by christophe.habib340 • written 2.6 years ago by BAB Lab40

Do you find a solution?

ADD REPLYlink written 2.4 years ago by cristianrohr76820

Did you find a solution for this problem ? I have the exact same error after upgrading Galaxy from release 16.01 to release 16.04.

ADD REPLYlink modified 2.4 years ago • written 2.4 years ago by christophe.habib340

Hi, Can you give us more informations about what you are trying to do ? What tool of GATK are you trying to run ? What are all the parameters in the wrapper this tools?

ADD REPLYlink written 2.6 years ago by christophe.habib340

Sure thing. I was attempting to use the Realigner Target Creator tool, although they all crash with the same error. From what I can tell, there's an xml wrapper for gatk that allows you to select an analysis type, which then calls wrappers for the individual tools once you make your selection. These individual tool wrappers each have their own sets of parameters appropriate to each tool. There is also a file called "gatk_macros.xml" included with this set of files that includes a set of parameters that appear to be common for all gatk runs. I'm guessing that's where the problem is, but I don't know for sure. Also, I'm pretty sure that this isn't coming from the Galaxy job runners because other tools are installing and running just fine.

ADD REPLYlink written 2.6 years ago by BAB Lab40

Yes I am a GATK3 user too as well. I mean, what are the exact parameters you use to launch your analysis of Realigner Target Creator ? Do you try to specify genomic interval ? Computational options ? and so on.

I would like to reproduce this bug to help you.

ADD REPLYlink written 2.6 years ago by christophe.habib340

Gotcha. So far, changing the parameters doesn't make a difference. In the screengrab linked below, you can see that I didn't set any of the optional parameters, just ran defaults for everything. No intervals specified, no BQSR, no comp. options. I did try setting some of the optional tool specific parameters as well (max. interval size = 900), it made no difference.

ADD REPLYlink modified 2.6 years ago • written 2.6 years ago by BAB Lab40
gravatar for Jennifer Hillman Jackson
2.6 years ago by
United States
Jennifer Hillman Jackson25k wrote:

Contacting the tool author is the best way to get help from here. Log into the tool shed and this will be an option in the top far right menu.

ADD COMMENTlink written 2.6 years ago by Jennifer Hillman Jackson25k

Yeah, I think you may be right. Thanks for the suggestion.

ADD REPLYlink written 2.6 years ago by BAB Lab40
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