Question: Using Gatk Queue on Galaxy tool
0
gravatar for kunaphas.kon
2.6 years ago by
Thailand
kunaphas.kon0 wrote:

I already build script using GATK queue , btw are there any specific tutorial that can guide me to set up my gatk queue to my local galaxy tool or just follow add-tool tutorial in galaxy document.

Any suggestion are most welcome 

Thank you, 

Note

gatk-queue galaxy gatk • 663 views
ADD COMMENTlink modified 2.6 years ago • written 2.6 years ago by kunaphas.kon0
0
gravatar for Jennifer Hillman Jackson
2.6 years ago by
United States
Jennifer Hillman Jackson23k wrote:

Hello,

Do you mean that you wish to create a Workflow in Galaxy to replicate the other script? I would suggest executing the steps first, then extracting a workflow. Then edit it to customize output names and such as desired. Here is some help to get you started: AdvancedWorkflow

Add tools from the Main Tool Shed as available and wrap any that are missing as the first step.

Best, Jen, Galaxy team

ADD COMMENTlink written 2.6 years ago by Jennifer Hillman Jackson23k
0
gravatar for kunaphas.kon
2.6 years ago by
Thailand
kunaphas.kon0 wrote:

Oh acttually , I mean  I already warp   variant calling process using GATK queue , and I want to apply it as a single box in galaxy tool ,but I don't know how to apply it because my script write in java  or I have to create another script to connect betweeon my GATK queue and galaxy ,btw I will take a look at your suggestion carfully.

thank you for your suggestion 

many thanks

Note

ADD COMMENTlink written 2.6 years ago by kunaphas.kon0

You can probably wrap your pipeline into Galaxy, I haven't seen any tool so far where this is not possible. But we appreciate any in updating our Galaxy wrappers.

Cheers,

Bjoern

ADD REPLYlink written 2.6 years ago by Bjoern Gruening4.8k
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