This is an annoyance when trying to use these tools interactively, but running or designing a workflow in the editor should work just fine. The issue is that for Galaxy the BAM index is technically considered an optional metadata attribute, but it is required for GATK. I've removed the metadata validator from the tool configurations and updated the GATK wrapper script to build missing BAM indexes on the fly as needed in changeset 6745:167fddae9646.

On Feb 24, 2012, at 6:57 PM, Curt Palm wrote:

When I try to run a GATK analysis that uses a bam file as input, I get the following error in the html page:

Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue.

when the input file is a bam file that has not run yet or is still running. So I can not set up multi step analysis or set up a work flow.

I searched the mailing lists and could not find info on this, only a thread discussing wanting to use meta data from bam files to set the ref. genomes for GATK tools.

is there a solution to this
I am using the current version of Galaxy.

thanks

*******************************************************
Curtis J. Palm cpalm@stanford.edu
Stanford Genome Technology Center

MC: 8307
office: 650-812-1994 cell: 408 858-7849
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