GATK 3 wrapper

Question: GATK 3 wrapper

3.5 years ago by

France

Hi everyone,

My question is quite simple, do you know someone who is working on a wrapper of GATK3.x ? I found here A: Galaxy GATK 2 installation error that Bjoern Gruening was working with the GATK dev team on this wrapper, and I also found this information here : http://gatkforums.broadinstitute.org/discussion/4519/gatk3-wrappers-for-galaxy

I found the development of the GATK2.0 on Bjoern github, but nothing regarding the GATK3.

Do you have any information about GATK3 wrapper development? Please let me know.

Thank you!

Christ

gatk • 1.1k views

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modified 2.7 years ago • written 3.5 years ago by christophe.habib • 340

2.8 years ago by

paolo.uva • 30

paolo.uva • 30 wrote:

Hi Christ,

I found a recent development of GATK 3 wrappers on the toolsked by avowinkel.

The development repository is here:

https://github.com/kaktus42/galaxytools/tree/master/tools/gatk

Cheers,

Paolo

ADD COMMENT • link written 2.8 years ago by paolo.uva • 30

I second this answer, we have the version from avowinkel deployed in our local galaxy.

While it isn't perfect, it does work.

ADD REPLY • link written 2.8 years ago by matthias.desmet • 150

Hello guys,

Thank you for your answer. Indeed I have found this wrapper and we are using it at my lab. I looked the wrapper itself and I found it really beautiful. Some options are missing so I had to modify it but we are really thankful to have it.

Cheers,

Christ

ADD REPLY • link written 2.8 years ago by christophe.habib • 340

Hi @christophe, @matthias and @Paolo. How can one use this wrapper? I tried accessing avowinkel's toolshed but there doesn't seem to be a way to actually start using GATK. Thanks for your input!

ADD REPLY • link written 6 months ago by carmeyeii89 • 0

3.5 years ago by

Bjoern Gruening ♦ 5.1k

Germany

Bjoern Gruening ♦ 5.1k wrote:

Christoph, no progress yet. Due to the strange GATK licensing this is has no high priority for me. You can find the latest wrappers here:https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 and I think this would be a good place to start working on version 3. I also have some idea how to do the conversion automatically. Let me know you are interested on working on it.

Cheers,

Bjoern

ADD COMMENT • link written 3.5 years ago by Bjoern Gruening ♦ 5.1k

3.5 years ago by

christophe.habib • 340

France

christophe.habib • 340 wrote:

Hi Bjoern,

My lab really needs to use GATK3 for our diagnostics and the community would really benefit of this work. I am still a beginner in wrapper writing, but it will be one of my most common task in the future. So I am interested on working on it.

I am open to any suggestion regarding this work.

Cheers,

Christ

ADD COMMENT • link written 3.5 years ago by christophe.habib • 340

2.7 years ago by

christophe.habib • 340

France

christophe.habib • 340 wrote:

Hello everyone,

I will post here since I have an issue with one of the GATK3 wrappers that I don't really understand. I want to specify a VCF files with known indels (in the optionnal parameters). But it doesn't work and I have this error :

Traceback (most recent call last):
  File "/home/galaxy/lib/galaxy/jobs/runners/__init__.py", line 163, in prepare_job
    job_wrapper.prepare()
  File "/home/galaxy/lib/galaxy/jobs/__init__.py", line 862, in prepare
    self.command_line, self.extra_filenames, self.environment_variables = tool_evaluator.build()
  File "/home/galaxy/lib/galaxy/tools/evaluation.py", line 422, in build
    raise e
NotFound: cannot find 'consensusDeterminationModel' while searching for 'analysis_type.consensusDeterminationModel'

So I looked to the wrapper indel_realigner.xml. From what I see the consensusDeterminationModel is well determined in the macro_optional_parameters with the right values, and then the block analysis_type.optional_parameters.optional_parameters_enabled seems to be OK as well. And there is no spelling errors.

Why this options is not found by the wrapper ? I see nothing that could explain this error :(

ADD COMMENT • link modified 2.7 years ago • written 2.7 years ago by christophe.habib • 340

Ok I just found what was wrong. Line 74 and 75 :

    --consensusDeterminationModel       ${analysis_type.consensusDeterminationModel}
    --LODThresholdForCleaning           ${analysis_type.LODThresholdForCleaning}

Should be :

    --consensusDeterminationModel       ${analysis_type.optional_parameters.consensusDeterminationModel}
    --LODThresholdForCleaning           ${analysis_type.optional_parameters.LODThresholdForCleaning}

My bad, I didn't read properly before I made my post.

ADD REPLY • link written 2.7 years ago by christophe.habib • 340

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