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Start Command

The Flux Capacitor provides a wrapper script to launch the program from predominant shell interpreters of major platforms.

shell

(Linux/Unix)

$ flux-capacitor

cmd

(Windows)

 C:\>flux-capacitor.bat -t capacitor

When started without parameters, the Flux Capacitor provides a list of command line flags that can be provided when starting the program.

Flux-Capacitor v1.0.3-SNAPSHOT (Flux Library: 1.15-SNAPSHOT)

[ERROR] 
[ERROR] No parameter file specified!
[ERROR] 

The Flux Capacitor

Tool specific options
  [(-p|--parameter) <file>] 				specify parameter file (PAR file)
  [(-a|--annotation) <gtf>] 				Path to the annotation file
  [(-i|--input) <bed>] 						Path to the mapping file
  [(-o|--output) <gtf>] 					Path to the output file
  [(-m|--annotation-mapping) <mapping>]		Annotation Mapping (default PAIRED) (default: PAIRED)
  [(-d|--read-descriptor) <descriptor>] 	Read Descriptor (default PAIRED) (default: PAIRED)
  [-r|--sort-in-ram]						Sort in RAM
  [--printParameters] 						Print default parameters

Parameter

As can be seen by the default output above, the Flux Capacitor requires a parameter file to be specified by the command line flag "-p". A parameter file contains a list of parameter/value pairs, one per line and separated from each other by white spaces. An overview of parameters that can be contained in the parameter file with explanations and their respective default values is output with the flag "--printParameters".

$ flux-capacitor --printParameters
Flux-Capacitor v1.0.3-SNAPSHOT (Flux Library: 1.15-SNAPSHOT)

# The annotation file
#
ANNOTATION_FILE    

#  Information from the read descriptor that will be used for annotation mapping
#
# [PAIRED, STRANDED, SINGLE, COMBINED] default: SINGLE
ANNOTATION_MAPPING    SINGLE

#...

The remaining command line flags "-x", "-l", and "-s" are to specify which steps of the simulation pipeline described in the parameter file are to be carried out: simulated expression of a random transcriptome ("-x"), simulated library construction ("-l"), and/or simulated sequencing ("-s"). The next section introduces the pre-requirements, the algorithms, and the parameters for each pipeline step.

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