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Question: Database Schema
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gravatar for Nils Homer
8.6 years ago by
Nils Homer • 40
Nils Homer • 40 wrote:
Could someone point me to the documentation for the sql-lite schema used in Galaxy? I would like to set up a mysql database and I am looking for instructions on how to get it working with Galaxy with the correct schema. Sincerely, Nils Homer
galaxy • 1.3k views
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modified 8.6 years ago by Nate Coraor ♦ 3.2k • written 8.6 years ago by Nils Homer • 40
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gravatar for Nate Coraor
8.6 years ago by
Nate Coraor ♦ 3.2k
United States
Nate Coraor ♦ 3.2k wrote:
Hi Nils, If you don't need to migrate any data, you can simply direct Galaxy to your new (empty) database, and it'll automatically populate it. --nate
ADD COMMENT • link written 8.6 years ago by Nate Coraor ♦ 3.2k
I apologize for my many questions, but I am really excited about potentially setting up galaxy. How are complicated workflows modeled and implemented (xml?) for a PBS/SGE cluster? For example, suppose I have a billion reads from a NGS technology, and I want to go from the raw files to variant calls etc. In our manual pipeline, we parallelize across our cluster by splitting the data (in the map/reduce model) for each step (file-conversion/alignment/merging/duplicate/removal/variant- calling/annotat ion etc.). There are many dependencies and merge and forks. Does galaxy handle this itself or how would I do this with galaxy?
ADD REPLY • link written 8.6 years ago by Nils Homer • 40
Hi Nils, Currently most structure parallelism in Galaxy is at the between tool level, individual tool runs still usually run on a single node. There are certain tools that manage their own parallelism. We're currently working on better support for within job parallelism, and in particular extending our tool configuration to support tools that use different models for parallelism, from loosely coupled, to map reduce, to MPI. We'd definitely appreciate your suggestions. Thanks, James
ADD REPLY • link written 8.6 years ago by James Taylor • 320
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