Scripts interacting with the database
Sorry for being really verbose on this list recently, but we are making a huge push for Galaxy right now. Hopefully you all aren't annoyed by me yet...! One thing we want to do after a MiSeq run is to run all assemblies and then report certain statistics such as N50. These metrics would then be reported in an exportable spreadsheet for our molecular biologists. I have the scripts ready to calculate these metrics. My questions here are: 1) Is there any kind of existing functionality that is close to what I want? 2) If not, 2a) Is there a way to trigger some scripts for assembly and metrics (and maybe more) once a MiSeq dumps all the data into Galaxy? 2b) Is there a certain convention on interaction with the database? And documentation on that? 2c) Is there an existing convention on reading the Galaxy database, so that I can produce the spreadsheet? Documentation? 2d) Our lab would call this functionality Rover, since it will roam Galaxy looking for and retrieving data (not really a question, but I thought they came up with a good name!) -- Lee Katz, Ph.D.
1) Is there any kind of existing functionality that is close to what I want?
Depending on whether you are using stock Galaxy or nglims, and how you are getting data into Galaxy, there are various ways to do it. For Galaxy's stock sample tracking, you can setup workflows to trigger automatically when data arrives. However, what I suspect is that you want to use the Galaxy API for this. There should never be a need to interact directly with the database, you should be able to do everything you want using the REST APIs. There should be an example script included with Galaxy that watches a directory for datasets, loads them into Galaxy, and runs a workflow using the API.
2) If not, 2a) Is there a way to trigger some scripts for assembly and metrics (and maybe more) once a MiSeq dumps all the data into Galaxy? 2b) Is there a certain convention on interaction with the database? And documentation on that? 2c) Is there an existing convention on reading the Galaxy database, so that I can produce the spreadsheet? Documentation? 2d) Our lab would call this functionality Rover, since it will roam Galaxy looking for and retrieving data (not really a question, but I thought they came up with a good name!)
-- Lee Katz, Ph.D.
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participants (2)
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James Taylor -
Lee Katz