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* Some settings can be defined both in the configuration file and on the GotCloud command-line
 
* Some settings can be defined both in the configuration file and on the GotCloud command-line
 
** command-line options take priority over configuration file settings
 
** command-line options take priority over configuration file settings
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* A KEY can be used in another KEY's value by specifying $(KEY)
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** Example:
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**: <code>KEY1 = value1</code>
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**: <code>KEY2 = $(KEY1)/value2</code>
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*** When <code>KEY2</code> is used, it will be equal to: <code>value1/value2</code>
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====Output Directory====
'''Output Directory'''
   
* The output directory is required for running GotCloud, so GotCloud knows where to write its output
 
* The output directory is required for running GotCloud, so GotCloud knows where to write its output
 
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====Reference/Resource Files====
'''Reference/Resource Files'''
   
* See [[GotCloud: Genetic Reference and Resource Files]] for reference/resource file configuration settings
 
* See [[GotCloud: Genetic Reference and Resource Files]] for reference/resource file configuration settings
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====Cluster Configuration====
'''Cluster Configuration'''
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Regardless of the type of cluster system used, GotCloud will wait for each job to complete after launching it.
Regardless of the type of cluster system used, GotCloud will wait for each job to complete after launching it. GotCloud will launch the maximum number of jobs in parallel, and wait until one finishes before sending another job to the cluster system.
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* For any BATCH_TYPEs that run in batch mode, GotCloud generates a script that will wait until the step is complete before returning
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** In a sense, it "fakes" interactive mode for all batch types since it will not proceed until a command is finished
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* If you are at UM and are using flux, you can specify either <code>flux</code> or <code>pbs</code>
    
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