#File:batchList.doit
#"Revised: 9-26-2009"
#"Preprocess the data for the NIDDK/mAdb GSP Jak-Stat Prosector Database"
#
#"(1) Doing  GSP-InventoryExperiment Groups conversions and generating HTML pages"
data.GSPI-EG/params-GSPI-EG.map
data.GSPI-EG/params-GSPI-EG-concatTXT.map
data.GSPI-EG/params-GSPI-EG-concatHTML.map
data.GSPI-ExpGrp/params-GSPI-ExpGrp.map
data.GSPI-ExpGrp/params-GSPI-ExpGrp-exportBigCells.map
#
#"(2) Doing mAdb Retrieval Report conversions and generating HTML pages"
data.MRR/params-MRR.map
data.MRR/params-MRR-keep.map
#
#"(3) Doing JTV array name conversions and generating HTML pages"
###JTVinput/params-JTV.map
JTVinput/params-JTV-jtvReZip.map
#
#"(4) Convert Mapping .txt files to HTML"
data.Maps/params-Maps-EGMAP-html.map
data.Maps/params-Maps-ExperimentGroups-html.map
data.Maps/params-Maps-mAdbArraySummary-html.map
#
#"(5) Convert Mapping .txt files to .map files"
data.Maps/params-Maps-EGMAP-map.map
data.Maps/params-Maps-ExperimentGroups-map.map
data.Maps/params-Maps-mAdbArraySummary-map.map
##
#"(6) Doing mAdb and HTML conversion tests TODO generating HTML pages"
data.mAdb-TestsToDo/params-mAdb-TestsToDo.map
#
#"(7) Convert MRR all arrays to edited DB file."
#"    This is normally not done each time."
data.MRR-all/params-MRR-all-fastSave.map
data.MRR-all/params-MRR-all-fastMakeIndex.map
data.MRR-all/params-MRR-all-fastMakeStatisticsIndex.map
#
#"(8) Generate a Tests-Intersection .txt table and also the HTML for it."
#" from the mAdb-TestsToDo.txt data."
data.mAdb-TestsToDo/params-mAdb-TestsToDo.map
#
data.TestsIntersection/params-TestsIntersection.map
data.TestsIntersection/params-TestsIntersection-ALL-filter-LIT.map
data.TestsIntersection/params-TestsIntersection-ALL.map
#
#"(9) Flip several types of samples"
#"(9.1) Create Data file for Flip Tables."
#" Create edited Tables with Index-Maps."
#"  This is normally not done each time."
data.MRR-flip/params-MRR-all-fastSave.map
data.MRR-flip/params-MRR-all-fastMakeIndex.map
data.MRR-flip/params-MRR-all-fastMakeStatisticsIndex.map
#
#"(9.2) Flip Tables with and without filtering saving"
#" the flipped .txt file and .html file."
data.MRR-flip/params-MRR-flipGID-all-FeatureID.map
data.MRR-flip/params-MRR-flipGID-all-GeneList+FeatureID.map
data.MRR-flip/params-MRR-flipGID-all-GeneList-RowNames.map
data.MRR-flip/params-MRR-flipGID-all-GeneList+FeatureID-RowNames.map
#
#"(10) Create Data file for Flip Tables."
#" Create edited Tables with Index-Maps."
#"  This is normally not done each time."
data.search/params-search-fastSave.map
data.search/params-search-fastMakeIndex.map
data.search/params-search-fastMakeStatisticsIndex.map
#
#"(11) Run the GenBatchScripts to create the batch scripts data"
#"    This is normally not done each time."
data.GBS/params-genBatchScripts.map
#
#"(12) add index files in all directories so can copy to Web server "
data/params-dirIndexHtml.map
#
#"------------ End -------------"