Hi Joshua,

Is this on the main public site? If so, can you share your history with me and 
I'll take a look? If this is on a local instance, can you provide additional 
information, such as the GATK version that you are using?


Thanks for using Galaxy,

Dan

On Dec 11, 2012, at 5:34 PM, Joshua Orvis wrote:

> I'm having some problems with GATK as well, but do have a functional pipeline 
> that uses the following GATK tools in Galaxy:
> 
> - Realigner Target Creator
> - Indel Realigner
> - Unified Genotyper
> - Variant Filtration
> 
> The main problem I'm having with them is that it seems I need to run the 
> fasta/fastq groomer on all inputs before starting, and if I attempt to use 
> the 'advanced' options on either of the last two steps above it fails 
> immediately every time with a command-line option parsing error.  I plan on 
> digging into the wrapper script in the coming days in an attempt to correct 
> this, which is currently attributed to Dan Blankenberg.  I'm relatively new 
> to Galaxy development though and don't know where to submit my updates though 
> should I fix any of these problems.
> 
> Joshua
> 
> 
> 
> 
> On Tue, Dec 11, 2012 at 4:26 PM, Philipe Moncuquet <philippe.m...@gmail.com> 
> wrote:
> Hi,
> 
> I have encountered the same kind of errors. When I update the loc files link 
> to GATK, some of the tools display the reference genomes I added and some 
> not. It seems that the galaxy wrapper for GATK 1.6 is not very functional. 
> GATK don't really care because they are not supporting it any more, even 
> documentation has disappeared. And I understand that galaxy developers have 
> other stuff to do than supporting a tool that will disappear because it's not 
> open source any more. I don't know what tool could replace the recalibration 
> process done by GATK and don't know how to correct bugs neither. Any 
> suggestions ?
> 
> Philippe   
> 
> 
> 
> 2012/12/12 Farooq,Umar (res) <ufar...@resident.uchc.edu>
> Hi,
> 
> I am trying to incorporate GATK in my pipeline but not been able to make it 
> work. I aligned my data with Hg 19 and then ran sam tool filter and then 
> picard duplicate removal. I uploaded dbSNP and the reference FASTA file for 
> Hg 19 in galaxy to run this pipeline. But for some reason GATK tool for base 
> recalibration will not accept this output file. I wonder if there is sorting 
> or indexing issue but how to fix this in galaxy.
> 
> 
> An error occurred running this job: Picked up _JAVA_OPTIONS: 
> -Djava.io.tmpdir=/space/g2main [Mon Dec 10 10:30:42 EST 2012] 
> net.sf.picard.sam.CreateSequenceDictionary 
> REFERENCE=/space/g2main/tmp-gatk-tKp41A/gatk_input.fasta 
> OUTPUT=/space/g2main/tmp-gatk-tKp41A/dict3503196447953523717.tmp
> 
> Thanks,
> Umar
> 
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