Initial upgrade to Grails 2.x (2.0.4)
Update to new version (0.2). Make it require grails 2.0.4 or above.
Remove the plugin zip file. Update the .gitignore to ignore the new version of the zip file, plus other uneeded items.
Merge branch 'master' into grails2x
Add note that this is for grails 2x.
Move plugin dependencies to BuildConfig.groovy
Updates for build
Merge branch 'grails2x' into postgresMigrate

Conflicts:
	.classpath
	plugin.xml
	target/classes/BuildConfig.class
	target/classes/Config.class
	target/classes/DataSource.class
	target/classes/RdcRmodulesGrailsPlugin.class
	target/classes/UrlMappings.class
	target/classes/com/recomdata/transmart/data/association/BoxPlotController.class
	target/classes/com/recomdata/transmart/data/association/DataAssociationController.class
	target/classes/com/recomdata/transmart/data/association/MarkerSelectionController.class
	target/classes/com/recomdata/transmart/data/association/PCAController.class
	target/classes/com/recomdata/transmart/data/association/RHClustController.class
	target/classes/com/recomdata/transmart/data/association/RHeatmapController.class
	target/classes/com/recomdata/transmart/data/association/RKMeansController.class
	target/classes/com/recomdata/transmart/data/association/RModulesController.class
	target/classes/com/recomdata/transmart/data/association/RModulesOutputRenderService.class
	target/classes/com/recomdata/transmart/data/association/RModulesService.class
	target/classes/com/recomdata/transmart/data/association/ScatterPlotController.class
	target/classes/com/recomdata/transmart/data/association/SurvivalAnalysisController$_closure2.class
	target/classes/com/recomdata/transmart/data/association/SurvivalAnalysisController$_closure2_closure5.class
	target/classes/com/recomdata/transmart/data/association/SurvivalAnalysisController$_closure2_closure6.class
	target/classes/com/recomdata/transmart/data/association/SurvivalAnalysisController$_closure3.class
	target/classes/com/recomdata/transmart/data/association/SurvivalAnalysisController$_closure3_closure7.class
	target/classes/com/recomdata/transmart/data/association/SurvivalAnalysisController$_closure4.class
	target/classes/com/recomdata/transmart/data/association/SurvivalAnalysisController$_closure4_closure8.class
	target/classes/com/recomdata/transmart/data/association/SurvivalAnalysisController$_closure4_closure8_closure9.class
	target/classes/com/recomdata/transmart/data/association/SurvivalAnalysisController.class
	target/classes/com/recomdata/transmart/data/association/TableWithFisherController.class
	target/classes/com/recomdata/transmart/data/association/asynchronous/RModulesJobService.class
	target/classes/com/recomdata/transmart/data/association/pdf/PDFController.class
	web-app/Rscripts/PCA/LoadPCA.R
Remove target.
Comment out reference to self.
merged branches grails2x, RC2 and postgresMigrate
Adding help links.
TSMTGPL-5 - Adding a check to make sure the survival time field is numeric. If it isn't, commas are stripped out and an attempt is made to coerce the column into a numeric.
adding a .gitattributes file to specify automatic handling of line endings
Still a lot of line endings to be fixed
Merge branch 'postgresMigrate' of https://github.com/thehyve/Rmodules into postgresMigrate

Conflicts:
	.classpath
	web-app/Rscripts/ANOVA/BuildANOVAData.R
	web-app/Rscripts/Heatmap/HClusteredHeatmapLoader.R
	web-app/Rscripts/LineGraph/BuildLinearData.R
	web-app/Rscripts/LineGraph/LineGraphLoader.r
	web-app/Rscripts/TableWithFisher/BuildFisherData.R
Merge branch 'master' of https://github.com/transmart/Rmodules into postgresMigrate

Conflicts:
	.classpath
	grails-app/controllers/com/recomdata/transmart/data/association/IC50Controller.groovy
	grails-app/controllers/com/recomdata/transmart/data/association/TableWithFisherController.groovy
	grails-app/controllers/com/recomdata/transmart/data/association/WaterfallController.groovy
	grails-app/views/plugin/BoxPlot.gsp
	grails-app/views/plugin/CorrelationAnalysis.gsp
	grails-app/views/plugin/IC50.gsp
	grails-app/views/plugin/LineGraph.gsp
	grails-app/views/plugin/SurvivalAnalysis.gsp
	grails-app/views/plugin/TableWithFisher.gsp
	grails-app/views/plugin/Waterfall.gsp
	grails-app/views/plugin/_ic50_out.gsp
	grails-app/views/plugin/_waterfall_out.gsp
	web-app/Rscripts/ANOVA/BuildANOVAData.R
	web-app/Rscripts/Common/dataBuilders.R
	web-app/Rscripts/Heatmap/HClusteredHeatmapLoader.R
	web-app/Rscripts/IC50/BuildIC50Data.R
	web-app/Rscripts/IC50/IC50Loader.R
	web-app/Rscripts/LineGraph/BuildLinearData.R
	web-app/Rscripts/LineGraph/LineGraphLoader.r
	web-app/Rscripts/MarkerSelection/BuildMSData.R
	web-app/Rscripts/PCA/BuildPCAData.R
	web-app/Rscripts/PCA/LoadPCA.R
	web-app/Rscripts/Survival/SurvivalCurveLoader.r
	web-app/Rscripts/TableWithFisher/BuildFisherData.R
	web-app/Rscripts/TableWithFisher/FisherTableLoader.R
	web-app/Rscripts/Waterfall/BuildWaterfallData.R
	web-app/Rscripts/Waterfall/WaterfallPlotLoader.R
	web-app/js/plugin/BoxPlot.js
	web-app/js/plugin/LineGraph.js
	web-app/js/plugin/SurvivalAnalysis.js
	web-app/js/plugin/TableWithFisher.js
Up to Grails 2.2.0, add plugin.xml to .gitignore
Merge pull request #1 from thehyve/postgresMigrate

Postgres migrate update from Kees
Update grails-app/conf/BuildConfig.groovy

Adding mavenRepo for ehcache-core