Question: GATK in Galaxy Main
gravatar for David Wilson
2.9 years ago by
David Wilson30
David Wilson30 wrote:

Dear Glaxy Main admins,

I just noticed that GATK tools available in the main Galaxy server 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


main tools galaxy gatk freebayes • 1.4k views
ADD COMMENTlink modified 2.9 years ago by Jennifer Hillman Jackson25k • written 2.9 years ago by David Wilson30
gravatar for Jennifer Hillman Jackson
2.9 years ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello David,

This is true, the version of the wrapped GATK tools available at 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 COMMENTlink modified 6 months ago • written 2.9 years ago by Jennifer Hillman Jackson25k

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

ADD REPLYlink written 4 months ago by Jennifer Hillman Jackson25k
gravatar for Bjoern Gruening
2.9 years ago by
Bjoern Gruening5.1k
Bjoern Gruening5.1k 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.



ADD COMMENTlink written 2.9 years ago by Bjoern Gruening5.1k
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