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
Nils Homer 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.
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
Sincerely,
Nils Homer
_______________________________________________ galaxy-user mailing list galaxy-user@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-user
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? On 5/4/10 1:06 PM, "Nate Coraor" <nate@bx.psu.edu> wrote:
Nils Homer 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.
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
Sincerely,
Nils Homer
_______________________________________________ galaxy-user mailing list galaxy-user@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-user
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 On May 4, 2010, at 4:47 PM, Nils Homer wrote:
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?
participants (3)
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James Taylor -
Nate Coraor -
Nils Homer