setting dbkey in a workflow

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setting dbkey in a workflow

Will Holtz
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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Re: setting dbkey in a workflow

Jen Hillman-Jackson
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


___________________________________________________________
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:

  http://lists.bx.psu.edu/listinfo/galaxy-dev

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

  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:

  http://galaxyproject.org/search/mailinglists/

-- 
Jennifer Hillman-Jackson
http://galaxyproject.org

___________________________________________________________
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:

  http://lists.bx.psu.edu/listinfo/galaxy-dev

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

  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:

  http://galaxyproject.org/search/mailinglists/
Jennifer Hillman-Jackson
http://galaxyproject.org