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.mcqt@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) <UFarooq@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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___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

  http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

  http://lists.bx.psu.edu/

___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

 http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

 http://lists.bx.psu.edu/