I'm working on making my first workflow in Galaxy, using a local server. A high 
level overview of the workflow is:
1) take a fasta file as input with dbkey set to organism1
2) blast input fasta file against organism2 database
3) manipulate the blast output into bed format
4) extract genomic DNA from organism2 based on the bed data

I can't find a way to set the dbkey on the bed data to organism2. This results 
in the extract genomic DNA step failing, as it seems to default to the only 
dbkey that exists in my workflow, the dbkey from the input fasta file. (The 
names and intervals are not present in the organism1 genome, and thus the 
extract step fails.) 

I have found that if I set my the dbkey of my input fasta file to be organism2 
(even though the sequences contained in it are actually from organism1), then 
my workflow successfully completes with the desired output. But this is a bit 
of a hack. I'd like to share my workflow with some coworkers and make it as 
easy to use as possible. Therefore I don't want to have to explain this hack to 

Is it possible to set the dbkey within a workflow?

thanks in advance for your help!

The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:


To manage your subscriptions to this and other Galaxy lists,
please use the interface at:


To search Galaxy mailing lists use the unified search at:


Reply via email to