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:



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