NAME

SYNOPSIS

  runGapResolution.pl [options] <aceFile> <454Scaffolds.txt> <454NewblerMetrics>
    <454AllContigs.fna> <454AllContigs.qual>
  Options:
  -od <path>    Output directory (optional; default is current dir)
  -np <number>  Specify number of parallel processes to use (optional; default is non-parallelized mode)
  -p <name>     Used for naming primers (optional)
  -pd <path>    Absolute full path to phd_dir for Sanger data (optional)
  -c <file>     Config file (optional; default is either specified using environment variable GAPRES_CONFIG or in installation path)
  -h            Detailed message (optional)

DESCRIPTION

Head wrapper to execute the Gap Resolution sub system.

DEPENDENCIES

The following scripts (configurable in config file) must exist in the same path as runGapResolution.pl unless the path to the script is defined in the config file:

  * createGapResProject.pl
  * idContigRepeats.pl
  * getSubProjReads.pl
  * newblerAssemSubProject.pl
  * validateSubProject.pl
  * createSubProjectPrimers.pl
  * createAnchorTagsForAce.pl

A default config file named gapRes.config residing in <installPath>/config is used to specify the following parameters:

  script.createGapResProject=createGapResProject.pl
  script.idContigRepeats=idContigRepeats.pl
  script.getSubProjReads=getSubProjReads.pl
  script.newblerAssemSubProject=newblerAssemSubProject.pl
  script.validateSubProject=validateSubProject.pl
  script.createSubProjectFakes=createSubProjectFakes.pl
  script.createSubProjectPrimers=createSubProjectPrimers.pl
  script.createAnchorTagsForAce=createAnchorTagsForAce.pl
  script.createAnchorTagsForSubprojectAce=createAnchorTagsForSubprojectAce.pl
  runGapResolution.addAnchorTagsToMainAceFile=1
  runGapResolution.addAnchorTagsToSubprojectAceFile=1
  
  The specify individual software components to run, modify the following
  parameters in the config file, setting 1 to execute, 0 to skip.
  
  execute.createGapResProject.pl=1
  execute.idContigRepeats.pl=1
  execute.getSubProjectReads.pl=1
  execute.newblerAssemSubProject.pl=1
  execute.validateSubProject.pl=1
  execute.createSubProjectPrimers.pl=1 
  execute.createAnchorTagsForAce.pl=1
  execute.createAnchorTagsForSubprojectAce.pl=1
  
To specify your own config file, set the environment variable GAPRES_CONFIG to
the path and name of the file.

VERSION

$Revision$

$Date$

AUTHOR(S)

Stephan Trong

HISTORY