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
them.
Is it possible to set the dbkey within a workflow?
thanks in advance for your help!
-Will
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