gsRunProcessor executable

6.1	gsRunProcessor executable

The gsRunProcessor command is not designed to be called directly by users but is primarily called from a launching script, by the gsRunProcessorManager or by a third-party job scheduling system such as SunGrid or PBS. The launching scripts handle all the job set-up, directory creation, and the launching of the gsRunProcessor executable itself. When the gsRunProcessor is called directly, its command line structure and arguments are as described below.

gsRunProcessor --prep [OPTIONS] sourceDirectory

gsRunProcessor --pipe=PIPELINE [OPTIONS] sourceDataFiles

Command	Description
gsRunProcessor	Runs image and/or signal processing algorithms, beginning with either the raw image files (.png or legacy .pif) or the output of the image processing step (the .cwf files) based on the processing launch script and pipeline processing script that invoked it.

Argument	Description
--prep	Either reads an existing dataRunParams.xml input XML file or creates one from the imageLog.parse and image files in the sourceDirectory and prepares the directory structure needed (D_ folder, regions and sff sub-folders) for the processing output.
sourceDirectory	Data directory containing files to be processed.
--pipe=XMLFILE	Specifies a pipeline processing script file. (Specifying the .xml extension is optional.)
sourceDataFiles	Data files to be processed.

Option	Description
--reg=REGION_NUM	Specifies which PTP regions to analyze (e.g. ‘1-3,5’)
-pXMLFILE, --pipe=XMLFILE	Specifies a pipeline processing script file (Specifying the .xml extension is optional.)
-rXMLFILE, --run=XMLFILE	Specifies a metadata file ( i.e. dataRunParams.xml)
-iIMAGELOG, -imageLog=IMAGELOG	Specifies image information (i.e. imageLog.parse)
--analysisParms=FILE	Specifies the location of analysisParms.parse
-rDIR, --images=DIR	Specifies the raw image path
-lDEST, --log=DEST	Specifies the log file destination
-eDEST, --error=DEST	Specifies the error file destination
-oDIR, --out=DIR	Specifies the output directory
--intermediate[=type]	Outputs intermediate files(Type=wells or cwf)
-f, --force	Forces overwriting of output files
-u, --useDisk	Uses disk-backed storage to allow processing of larger data sets
-tTIME, --timeout=TIME	Specifies a timeout for waiting for new images
-nNAME, --name=NAME	Sets the processing job "name"
-jJOBID, --job=JOBID	Overrides the automatic job ID creation
-T[XMLTEMPLATE], --template[=XMLTEMPLATE]	Creates a template XML script file of the type specified to standard output (e.g. ‘--template=filterOnly > filterTemplate.xml’)
--remoteProgress [=HOST:PORT]	Sends progress information to an XML-RPC server like gsRunProcessorManager
--list[=ARG]	Lists choices for an option (e.g. ‘--list=template’)
--mpi	Displays the MPI implementation (number of processors that will be used for the Run)
-v, --verbose	Sends detailed messages to console & output files
-q, --quiet	Suppresses normal console messages
-P, --progress	Sends progress messages to the console
-V, --version	Displays the version of the software
-h, --help	Display available help information

There are a few of environmental variables that can be used to fine tune the gsRunProcessor’s operation. Administrators and/or users do not normally need to set these variables after installation, however, when needed they can be used to locally define the environment variables for advanced users or special situations by inserting an environmental variable definition in a local or user’s .bash_profile script. Site administrators may choose to adjust these values site-wide by editing /etc/profile or by adding a file in the /etc/profile.d directory.

Environmental Variable	Description
PIPELINE_PATH	Adds additional path for pipeline scripts. A colon (:) is used to separate paths when specifying more than one.
PHRED_TABLES_PATH	Overrides the default location of the .dat files used for PHRED based quality scoring.
LEGACY_DN_PATH	Adds additional path for legacy .dn files. A colon (:) is used to separate paths when specifying more than one.