net.maizegenetics.analysis.gbs

Class ProductionPipelineMain

java.lang.Object

net.maizegenetics.analysis.gbs.ProductionPipelineMain

public class ProductionPipelineMain
extends Object

This class is for running the GBS Production Pipeline. It is to be run from within the sTASSEL.jar. The cron job should be set up to run the run_pipeline.pl which has been modified to make this class the main() to be run. The JVM memory settings within run_pipeline.pl should also be adjusted upwards. cron example 20 3 * * * cd /workdir/tassel/tassel4-src && /usr/local/bin/perl /workdir/tassel/tassel4-src/run_prod_cron.pl >> /workdir/tassel/tassel4-src/20130808_cron.log 2>&1 20130718 Note from Jeff Glaubitz: A minor detail: ProductionSNPCallerPlugin needs the key file name to end with "_key.txt". All the output files are named after the key file but replacing "_key.txt" with the appropriate extension. User: dkroon Date: 4/8/13

Field Summary

Fields

Modifier and Type	Field and Description
static String	applicationConfiguration

Constructor Summary

Constructors

Constructor and Description
ProductionPipelineMain(String appPropertiesFile, boolean runCheckSum, boolean runImputation, String testingCheckSum)

Method Summary

Modifier and Type	Method and Description
static String	compareOriginalAgainstImputed(String originalFile, String imputedFile) Generates basic summary information about imputation such as change in sites or taxa count change in missing data change in heterozygosity how many sites changed their major allele
static void	main(String[] args)

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

applicationConfiguration

public static String applicationConfiguration

Constructor Detail

ProductionPipelineMain

public ProductionPipelineMain(String appPropertiesFile,
                              boolean runCheckSum,
                              boolean runImputation,
                              String testingCheckSum)

Method Detail

compareOriginalAgainstImputed

public static String compareOriginalAgainstImputed(String originalFile,
                                                   String imputedFile)

Generates basic summary information about imputation such as change in sites or taxa count change in missing data change in heterozygosity how many sites changed their major allele

Parameters:

originalFile -

imputedFile -

Returns:

main

public static void main(String[] args)