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
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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participants (2)
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Jennifer Jackson -
William Holtz