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GotCloud: Alignment Pipeline (view source)

Revision as of 18:02, 23 October 2014

1,073 bytes removed ,  18:02, 23 October 2014
→‎Configuration File
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=== Configuration File ===  
 
=== Configuration File ===  
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Configuration file contains the run-time options including the software binaries and command line arguments.  A default configuration file is automatically loaded.  Users may specify their own configuration file specifying just the values different than the defaults.  The configuration file is not required if there are no values to override.
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{{:GotCloud: Configuration}}
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Comments begin with a <code>#</code>
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==== Additional Required Settings ====  
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Format: KEY = value
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Where KEY is the item being set and value is its new value
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See [[#Command-Line Options|Command-Line Options]] for values that can be set either via command line or via configuration.
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Note: Command-line options take priority over configuration file settings
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==== Required Settings ====  
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See [[#Reference Files|Reference Files]] for the required reference file settings.
      
See [[#FASTQ List File|FASTQ List File]] for how to set the index file either via command line options or via configuration.
 
See [[#FASTQ List File|FASTQ List File]] for how to set the index file either via command line options or via configuration.
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** Fill in the N with the number of threads you want BWA to run with, default is 1  
 
** Fill in the N with the number of threads you want BWA to run with, default is 1  
 
* SORT_MAX_MEM = 2000000000  
 
* SORT_MAX_MEM = 2000000000  
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** Maximum amount of memory used by samtools sort after running bwa  
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** Maximum amount of memory used by samtools sort after running bwa
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*BATCH_TYPE = type
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** Tells GotCloud to use "type" for sending jobs to the cluster
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** "type" can be mosix, slurm, slurmi, pbs, sge, sgei
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*BATCH_OPTS = options
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** replace "options" with the options you want to pass to your cluster type
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** For example: BATCH_OPTS = -j36,37,38,39,40,41,45,46,47,48,49
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*** Specifies which client nodes mosix should send jobs to.
      
== Running the Alignment Pipeline ==  
 
== Running the Alignment Pipeline ==  
Retrieved from "http://genome.sph.umich.edu/wiki/Special:MobileDiff/11864"

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