8f85cfb621850ffe710909abca6d8d91cd1b8929
kate
  Thu Aug 25 13:02:46 2016 -0700
Add hg38 tables to Gene Sorter. refs #17288

diff --git src/hg/near/makeNear.doc src/hg/near/makeNear.doc
index c323852..a5607ae 100644
--- src/hg/near/makeNear.doc
+++ src/hg/near/makeNear.doc
@@ -624,47 +624,51 @@
   > affyExonTissuesGs.ra
 grep -A5 affyExonTissuesAll ~/hg/makeDb/hgCgiData/Mouse/microarrayGroups.ra \
   | grep names | sed 's/^names //; s/,$//' | tr ',' '\n' \
   | awk 'BEGIN{OFS="\t"; id=0;}{ print id, $1, $1, "n/a", "n/a", "n/a", "3", "n/a,n/a,"$1","; id = id + 1;}' > all.expRecords
 hgLoadSqlTab mm8 affyExonTissuesGsExps expRecord.sql all.expRecords
 hgMedianMicroarray mm8 affyExonTissuesGs mm8.affyExonTissuesGsExps \
    affyExonTissuesGs.ra affyExonTissuesGsMedian mm8.affyExonTissuesGsMedianExps
 hgExpDistance mm8 affyExonTissuesGsMedian \
    affyExonTissuesGsMedianExps affyExonTissuesGsMedianDist
 
 ###############################################################
 ## GTEx
 ## (2016-08-16, kate)
 
 # Create a table that maps between known genes and GTEx (GENCODE V19) gene ids
-#hgMapToGene "-type=bed 12" hg19 gtexGeneModel knownGene knownToGtex
 cd /hive/data/genomes/hg19/bed/gtex
+
 #hgMapToGene hg19 -type=genePred gtexGeneModelV6 knownGene knownToGtex
 hgMapToGene hg19 -noLoad -all -type=genePred gtexGeneModelV6 knownGene knownToGtex.all
 hgMapToGene hg19 -all -type=genePred gtexGeneModelV6 knownGene knownToGtex
 
 #hgMapToGene hg38 -type=genePred gtexGeneModelV6 knownGene knownToGtex
 hgMapToGene hg38 -all -type=genePred gtexGeneModelV6 knownGene knownToGtex
 
 # Create expression distance table from median table.  This will take about an hour.
 #cd ~/src/hg/near/hgExpDistance
 # TODO: Consider adding weights file
 
 hgsql hgFixed -e select 1.0, id, name from gtexTissue > gtex.weights
 # edit to downweight brain (13 tissues total)
 
 hgExpDistance hg19 -verbose=2 -lookup=knownToGtex -weights=gtex.weights \
         hgFixed.gtexTissueMedian hgFixed.gtexTissue \
-                gtexDistance2 >&! distance2.log &
+                gtexDistance
+
+hgExpDistance hg19 -verbose=2 -lookup=knownToGtex -weights=gtex.weights \
+        hgFixed.gtexTissueMedian hgFixed.gtexTissue \
+                gtexDistance
 
 # Create ratio table.  
 # TODO: Consider adding -clump file
 # Defaults for microarray are too high -- RPKM is significant >2 roughly
 hgRatioMicroarray -minAbsVal=2 -minMaxVal=5 -database=hgFixed gtexTissueMedian gtexTissueMedianRatio2
 
 # Get max scores for columnDb.ra
 hgMaxExp hgFixed gtexTissueMedian
 # 219385.91
  
 hgMaxExp hgFixed gtexTissueMedianRatio
 # 12.53