Base Recalibration Tool On Usegalaxy

Question: Base Recalibration Tool On Usegalaxy

4.6 years ago by

KS • 40

KS • 40 wrote:

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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modified 4.6 years ago by Bjoern Gruening ♦ 5.1k • written 4.6 years ago by KS • 40

4.6 years ago by

Bjoern Gruening ♦ 5.1k

Germany

Bjoern Gruening ♦ 5.1k wrote:

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:

ADD COMMENT • link written 4.6 years ago by Bjoern Gruening ♦ 5.1k

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&adv anced_search=false&operation=view_or_manage_repository&page=1&async=fa lse&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.gruening@gmail.com>:

ADD REPLY • link written 4.6 years ago by KS • 40

Hi Kaz, We do have a problem with the Table Recalibration tool on Main right now. Well let you know when we have a fix. Thanks for using Galaxy, Dan

ADD REPLY • link written 4.6 years ago by Daniel Blankenberg ♦♦ 1.7k

Hi Dan, Thank you for informing. I know I should install my own local galaxy server for repetitive analyses, but this is the first time for me to analyse exome. Thank you for giving me opportunity to use galaxy in public. Hoping recovery of Table Recalibration tool. Regards, Kaz 2014-04-12 13:08 GMT+09:00 Daniel Blankenberg <dan@bx.psu.edu>:

ADD REPLY • link written 4.6 years ago by KS • 40

4.6 years ago by

Daniel Blankenberg ♦♦ 1.7k

United States

Daniel Blankenberg ♦♦ 1.7k wrote:

Hi Kaz, The issue with the Table Recalibration tool should now be resolved, youll need to refresh your Galaxy window if you havent already. Thanks for reporting the error and let us know if you find any more issues. Thanks for using Galaxy, Dan

ADD COMMENT • link written 4.6 years ago by Daniel Blankenberg ♦♦ 1.7k

Hi Dan, Thank you for your quick handling of the issue. It seems I have connection problem with usegalaxy now, but I will try Table Recalibration later. Thank you again. Regards, Kaz 2014-04-16 0:09 GMT+09:00 Daniel Blankenberg <dan@bx.psu.edu>:

ADD REPLY • link written 4.6 years ago by KS • 40

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