Hi Metge,

Thank you for your kind comments!

The GATK tool wrappers are still in an early beta stage of development. Because of this, we are not ready to support set-up in local instances yet.

If you have functionality input for the version on our Test server, general feedback is welcomed on the galaxy-...@bx.psu.edu mailing list.

Take care,

Jen
Galaxy team

On 11/16/11 3:29 PM, Metge, Franziska wrote:

Dear happy users of Galaxy,

We are running Galaxy locally. It's a very fine tool! By now everything
works fine, except when I try to run any GATK program. I usually get
this error message:


##### ERROR
------------------------------------------------------------------------------------------
##### ERROR A USER ERROR has occurred (version 1.3-14-g348f2db):
##### ERROR The invalid arguments or inputs must be corrected before the
GATK can proceed
##### ERROR Please do not post this error to the GATK forum
##### ERROR
##### ERROR See the documentation (rerun with -h) for this tool to view
allowable command-line arguments.
##### ERROR Visit our wiki for extensive documentation
http://www.broadinstitute.org/gsa/wiki
##### ERROR Visit our forum to view answers to commonly asked questions
http://getsatisfaction.com/gsa
##### ERROR
##### ERROR MESSAGE: The fasta file you specified (/tmp/tmpp0oxJu/hg19)
does not exist.
##### ERROR
------------------------------------------------------------------------------------------

my picard_index.loc line for the hg19 reference looks like this:


hg19 hg19 hg19 hg19 /drive1/galaxy/reference/hg19/sam_index/hg19_ref.fa gatk


also the bam file I am submitting to GATK has the reference genome
specified in it's attributes.

Could please anyone help me.
Thank you
Franzi



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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
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