Hi Will,
Agreed, this would make a useful Edit Step Actions function. More are
already planned and I asked our dev team to specifically consider this
as an enhancement in this Trello ticket:
https://trello.com/c/Gy0ZZpCc
If there if another work-around and I've missed it (development is a
fast, moving target!), we'll post an updated reply.
Best,
Jen
Galaxy team
On 4/5/14 11:09 PM, William Holtz wrote:
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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Jennifer Hillman-Jackson
http://galaxyproject.org
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The Galaxy User list should be used for the discussion of
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