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Step 6: Set up Distributed Computing

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fripp edited this page Feb 8, 2013 · 20 revisions

SMRT Analysis provides support for distributed computation using an existing job management system. Pacific Biosciences has explicitly validated Sun Grid Engine (SGE), LSF and PBS.

Note: Celera Assembler 7.0 will only work correctly with the SGE job management system. If you are not using SGE, you will need to deactivate the Celera Assembler protocols so that they do not display in SMRT Portal. To do so, rename the following files, located in common/protocols:

RS_CeleraAssembler.1.xml to RS_CeleraAssembler.1.bak
filtering/CeleraAssemblerSFilter.1.xml to CeleraAssemblerSFilter.1.bak
assembly/CeleraAssembler.1.xml to CeleraAssembler.1.bak

This section describes setup for SGE and gives guidance for extensions to other Job Management Systems.

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