Hi,

do you have access to the generated commandline from Galaxy and can
paste it her?

> 
> I’ve installed the latest version (using GATK2.8-1) of the GATK2
> wrapper here.  I’ve run into the following error:
> 
> ##### ERROR MESSAGE: The fasta file you specified
> (/tmp/tmp-gatk-V7IrBw) does not exist.
> 
>  
> 
> I see via much googling that this error is due to a user input
> problem.  I’ve tried pointing the gatk2_picard_index.loc file in
> tool-data to the proper data files:
> 
> hg19 hg19    hg19    /software/packages/galaxy/data/picard/hg19.fa

That look ok, as far as every token is separated by a tabular.

> 
> where the following files exist:
> 
> hg19.dict
> 
> hg19.fa
> 
> hg19.fa.fai

Can you put the 2bit file into the same folder?

Cheers,
Bjoern


> 
> I’m using a torque setup.  A bam file is being used as input.  After
> much trial and error I’ve been unable to figure out what I’m
> missing.  
> 
>  
> 
> None of the solutions on google apply to my situation.
> 
>  
> 
> Has anyone else run into this configuration problem and solved it?
> 
>  
> 
> Thanks,
> 
> -Sheldon
> 
>  
> 
> Sheldon Briand
> 
> NRC Research Computing Support Analyst
> 
> Research Computing Support / Soutien Informartique a la Recherche
> 
> Operations, Science Portfolio / Operations, Portefeuil des sciences
> 
> SSC-NRC / SPC-CNRC
> 
> Rm 329A, 1411 Oxford Street / Piece 329A, 1411 Rue Oxford
> 
> Halifax, NS  B3H 3Z1
> 
> 902 426-1677
> 
> sheldon.bri...@ssc-spc.gc.ca
> 
>  
> 
> 
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