Galaxy GATK 2 installation error

Question: Galaxy GATK 2 installation error

4.5 years ago by

do kadya • 130

do kadya • 130 wrote:

https://drive.google.com/file/d/0B6DXP2pIxiX7MW5UZHQ5UTR1Ukk/edit?usp=sharing
https://drive.google.com/file/d/0B6DXP2pIxiX7OUwweVZiLWVxVFE/edit?usp=sharing
https://drive.google.com/file/d/0B6DXP2pIxiX7Wm4xTTdJNm9FWVU/edit?usp=sharing

What is this error?

Why i am unable to install GATK2 in galaxy ?

Why its GATK 2 and not GATK 3 available for Galaxy ?

Waiting for positive reply.

Thank You.

- Chetan

software error galaxy gatk • 1.4k views

ADD COMMENT • link •

modified 4.5 years ago by Bjoern Gruening ♦ 5.1k • written 4.5 years ago by do kadya • 130

4.5 years ago by

do kadya • 130

do kadya • 130 wrote:

These are log files of GATK installation.

https://drive.google.com/file/d/0B6DXP2pIxiX7WVFpMHFQODd6dkE/edit?usp=sharing
https://drive.google.com/file/d/0B6DXP2pIxiX7YUxOUTc5UTBzOXc/edit?usp=sharing

I was trying this installation from 3-4 days. Today i restarted galaxy, uninstall old GATK2 (which was saying Cloning). Then went to tool shed, installed same with different name(GATK_2), and it got installed.

I don't know how it happen, as I was doing same from last 2-3 days.

Testing is still remaining.

ADD COMMENT • link written 4.5 years ago by do kadya • 130

4.5 years ago by

Bjoern Gruening ♦ 5.1k

Germany

Bjoern Gruening ♦ 5.1k wrote:

Hi,

are you running the latest Galaxy stable release? That error does not seem to be GATK related, rather than an old Tool Shed bug. GATK3 is not available, because no-one had time so far to adopt to the recent changes of GATK3. We are currently in contact with the GATK3 devs to streamline the Galaxy wrapper development a little bit and couple it to GATK releases. But that needs some time. If you want to help, here is the code:

https://github.com/bgruening/galaxytools/tree/master/gatk2

Pull requests welcome!

Bjoern

ADD COMMENT • link written 4.5 years ago by Bjoern Gruening ♦ 5.1k

Hi Bjoern,

In the galaxy logs, it shows these messages:

"galaxy.tools.data DEBUG 2014-06-14 00:19:44,635 Loading another instance of data table 'gatk2_annotations', attempting to merge content.
galaxy.tools.data DEBUG 2014-06-14 00:19:44,675 Loading another instance of data table 'gatk2_picard_indexes', attempting to merge content.
galaxy.tools.data DEBUG 2014-06-14 00:19:44,675 Loading another instance of data table 'gatk2_annotations', attempting to merge content.

galaxy.tools.data DEBUG 2014-06-14 00:19:44,675 Attempted to add fields (['AlleleBalance', 'AlleleBalance', 'AlleleBalance', 'UnifiedGenotyper,VariantAnnotator,VariantRecalibrator']) to data table 'gatk2_annotations', but this entry already exists and allow_duplicates is False."

PS: many such messages for different fields/tables are displayed.

It looks like some data is leftover from the previous failed installation which is conflicting with the newer installation. Any ideas how to deal with this?

ADD REPLY • link written 4.5 years ago by do kadya • 130

You can simply ignore it, or remove any left over files from the tool-data directory as you like.

Ciao,

Bjoern

ADD REPLY • link written 4.5 years ago by Bjoern Gruening ♦ 5.1k

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