On Thu, Jan 31, 2013 at 9:09 AM, Hakeem Almabrazi <halmabr...@idtdna.com> wrote:
>
> I was sure that was not the case (all in tabs).  Here is my bwa_indices.loc 
> file look like
> #####################
> #bwaReference   /usr/local/galaxy_data/hg19/bwa/
> hg19_reference_genome   
> /usr/local/galaxy_data/hg19/bwa/hg19_reference_genome.fasta
> #######################
>

This doesn't seem right, please take a look to the sample .loc file:
http://toolshed.g2.bx.psu.edu/repos/devteam/bwa_wrappers/file/ffa8aaa14f7c/tool-data/bwa_index.loc.sample

You need something like:
#<unique_build_id> <dbkey> <display_name> <file_path>
hg19 hg19 hg19 /depot/data2/galaxy/hg19/base/hg19.fa

Best,
Carlos
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