Hi Branden,

Vipin, thanks for the tip.  I was not aware of data tables at all.
>
> I checked bwa_wrapper.xml and it is still using the from_file attribute for
> the reference genome parameter, not from_data_table.  It would appear then
> that BWA is not using data tables?  Additionally, I have now noticed that
> our bowtie runs are failing as well with the error:
>

I am not sure about the below error message, based on the previous mail
error message
it is cleat that it is looking for a data_table type value instead of
from_file. I hope something
will be broken at your end when you pulled at last time.


>
> AssertionError: Requested 'path' column missing from column def
>
> I looked at bowtie_wrapper.xml, and it too seems to still be using
> from_file instead of from_data_table for the reference genome drop-down.
> There is a line there using data tables, but it is commented out:
>
> <!--<options from_data_table="bowtie_indexes"/>-->
>
> I'm really confused as to what is going on here, but it seems like when I
> updated recently (first time since January probably) it broke all of my
> location files and I'm not sure how to fix them.  I'm also confused because
> it seems that even using data tables, the format of my .loc files shouldn't
> need to change because they both use four columns separated by tabs.
>
> As always, any help is greatly appreciated.
>
>
I think probably the best idea to move everything to data_table based on
the documentation available in the Wiki page. Galaxy also recommending the
same.
If I found something useful, I will share with you.

regards, Vipin
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