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Question: Add Unified Genotyper to Local instance
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gravatar for braveen.joseph
14 months ago by
braveen.joseph • 20
braveen.joseph • 20 wrote:

HI There,

I tried to install the tool Unified Genotyper from the tool shed, and I was unable to do it.

Details follows,

Name: Unified Genotyper SNP and indel caller Type: Unrestricted Revision: 0 (2014-04-01) Owner : devteam

So I tried to add this tool manually into the galaxy local instance. I downloaded the tool from the following link. toolshed.g2.bx.psu.edu/repos/devteam/unified_genotyper/gatk_unified_genotyper/0.0.6

Then I followed the instructions provided by the galaxy in the following link. https://galaxyproject.org/admin/tools/add-tool-tutorial/

The tool showed up once in the Tool panel and doesn't show up anymore. Can someone please help me on this?

Thank you very much!!!
unified genotyper galaxy • 346 views
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modified 14 months ago • written 14 months ago by braveen.joseph • 20
0
gravatar for Jennifer Hillman Jackson
14 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

This tool has been deprecated for a few years now, only reached "beta" development stage, and is not recommended (nor any other GATK tools at this time). For alternatives, please see the Variant analysis tutorials and examples here: https://galaxyproject.org/learn/

Installing tools directly as admin using the GUI functions is recommended. But if you want to do advanced admin, the tutorial you reference is a bit older. Please see the current admin training materials here: https://github.com/galaxyproject/dagobah-training

Thanks, Jen, Galaxy team
ADD COMMENT • link written 14 months ago by Jennifer Hillman Jackson ♦ 25k
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gravatar for braveen.joseph
14 months ago by
braveen.joseph • 20
braveen.joseph • 20 wrote:

Thanks a lot for the reply!
ADD COMMENT • link written 14 months ago by braveen.joseph • 20
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