RunServerPipeline

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Run Server Pipeline Script

This command will invoke a Pipeline Script (PScript) registered on the Server similar the Pipeline block in a sample registration file.

Parameters

Required

  • Project.ID: Specify ID of the Server project to create or use (see AppendMode below)
  • ScriptID: Specify name of the .pscript file
  • SampleSetID: Comma delimited list of one or more IDs of existing SampleSets. A list of Sample IDs (must already be registered on Server) may also be supplied in lieu of a Set ID by enclosing in < >. For example, here we specify the IDs of 2 existing Sets (ProjectABC_cases and ProjectABC_controls and one temporal set of 3 Sample IDs:
SampleSetID=ProjectABC_cases,<ProjectDEF.Sample1,ProjectDEF.Sample2,ProjectXYZ.Sample1>,ProjectABC_controls
Tips.png See IA_AddSamples command to pre-register samples


Optional

Conditionally Required

These parameters may be required depending on the Server configuration (i.e. required project metadata fields) and Pipeline Script (i.e. required script parameters that don't have default values configured in the script)

Project Metadata

Project metadata values can be specified by prefixing the field ID with "Project.". For example, Description is often a required field so you would specify as:

Project.Description=Analysis of drug XYZ for atherosclerosis

PScript Parameters

The script's parameter values can be specified by prefixing the parameter ID with "Parameter.". For example, if the script defined a ThreadNumberPerJob parameter, you could specify as:

Parameter.ThreadNumberPerJob=4


Example Oscript

Begin ExecuteCommand /Namespace=Server;
Server "tcp://192.168.3.228:8065" /UserID=joseph /Password=OmicSoft123;
Command RunServerPipeline;
Options
"
Project.ID=drugXYZ_atherosclerosis
AppendMode=Replace
SampleSetID=ProjectABC_cases,<ProjectDEF.Sample1,ProjectDEF.Sample2,ProjectXYZ.Sample1>,ProjectABC_controls
ScriptID=C22078_RnaSeqPipeline_SM.pscript
Parameters.ReferenceName=Human.B37.3
Parameters.GeneModelName=OmicsoftGene20130723
Parameters.ResultsOutputFolder=/Users/joseph/drugXYZ_atherosclerosis/RNAseq
Parameters.ThreadNumberPerJob=2
Parameters.ParallelJobNumber=4
Parameters.PairedEnd=True
Parameters.ReplaceBam=True
CC=andrew.slater@qiagen.com
";
OutputFile "C:\Users\joseph\Documents\drugXYZ_atherosclerosis\oscripts\output\C22078_RnaSeqPipeline_SM.outfile";
End;


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Output

The OutputFile will report the ID of the Server job spawned by invoking the PScript

[JobID]
56cab543a911df15


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