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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