Hi Franzi,

You have one too many hg19 in there. The fields go like:
<unique_build_id>   <dbkey>   <display_name>   <fasta_file_path>        
<valid_tool_suites>
so:
hg19    hg19    hg19 /drive1/galaxy/reference/hg19/sam_index/hg19_ref.fa        
gatk

But do note that these tool integrations are still undergoing active 
development. Please report bugs if you encounter any.


Thanks for using Galaxy,

Dan


On Nov 16, 2011, at 6:29 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
> 
> ___________________________________________________________
> 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/

Reply via email to