GATK in Galaxy Main

Question: GATK in Galaxy Main

2.9 years ago by

Spain

Dear Glaxy Main admins,

I just noticed that GATK tools available in the main Galaxy server usegalaxy.org) now appear under the header "DEPRECATED". Does this mean that this tool suite it is not going to be updated? Will it be kept in the main server although deprecated? Some of us rely on this server and use these tools in our workflows, and therefore would suffer its loss.

Thanks in advance for your answer and support

David

main tools galaxy gatk freebayes • 1.4k views

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modified 2.9 years ago by Jennifer Hillman Jackson ♦ 25k • written 2.9 years ago by David Wilson • 30

2.9 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello David,

This is true, the version of the wrapped GATK tools available at http://usegalaxy.org will not be updated. Our team will follow up with more feedback about ongoing plans for supporting these tools on the server.

Take care! Jen, Galaxy team

ADD COMMENT • link modified 6 months ago • written 2.9 years ago by Jennifer Hillman Jackson ♦ 25k

Update: Some work is being done in the community now to update the GATK wrapper tool suite, using the latest version with improved open source licensing. Once completed, tested, and published, these will be added to the Galaxy ToolShed https://usegalaxy.org/tooolshed

ADD REPLY • link written 4 months ago by Jennifer Hillman Jackson ♦ 25k

2.9 years ago by

Bjoern Gruening ♦ 5.1k

Germany

Bjoern Gruening ♦ 5.1k wrote:

Hello David,

in this special case of GATK let me add that GATK has some licencing issues that prevents us from shipping the program to every in an automatic way. We (the IUC) tried hard to get this correct in our GATK 2.8 wrapper, which is part of the Tool Shed as Jen mentioned, but finally agreed to not spend to much effort in updating these tool suite as alternatives are equally good. For example have a look at freebayes.

Cheers,

Bjoern

ADD COMMENT • link written 2.9 years ago by Bjoern Gruening ♦ 5.1k

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