Hi Kaz,

We do have a problem with the Table Recalibration tool on Main right now. We’ll 
let you know when we have a fix.


Thanks for using Galaxy,

Dan


On Apr 11, 2014, at 10:24 PM, KS <k...@kyudai.jp> wrote:

> Hi Bjoern,
> 
> Thank you for the reply.
> 
> I found Table Recalibration, probably from GATK, on Tool Shed as you informed.
> http://toolshed.g2.bx.psu.edu/repository/view_repository?sort=name&advanced_search=false&operation=view_or_manage_repository&page=1&async=false&show_item_checkboxes=false&f-free-text-search=recalibration&id=797c55906a13241a
> But I am only a user of usegalaxy public server, so I am afraid I
> think I can't install tool from tool shed.
> 
> What I am doing is here:
> https://usegalaxy.org/u/ksfk/h/illumina-exome
> 
> I think I need Table Recalibration in "NGS: GATK Tools (beta)" tool
> group of left pane of usegalaxy, but I cannot find it.
> 
> I am wondering whether there is any way to directly call Table
> Recalibration without web-application wrapper.
> 
> Regards,
> Kaz
> 
> 2014-04-12 7:26 GMT+09:00 Björn Grüning <bjoern.gruen...@gmail.com>:
>> Hi Kaz,
>> 
>> you are searching for GATK tools, right? Please have a look at the GATK
>> suites in the Tool Shed.
>> 
>> Cheers,
>> Bjoern
>> 
>> Am 12.04.2014 00:16, schrieb KS:
>>> 
>>> Dear all,
>>> 
>>> I can't find either of Table Recalibration or Base Recalibrator on
>>> usegalaxy public server. I am defident this is right place to ask, but
>>> seqanswers is clouded with many other pipelines.
>>> 
>>> Is there an update of base recalibration tool on usegalaxy?
>>> 
>>> Best,
>>> Kaz
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