5bcbbd0c26d71a17b7eae9f8a138f0e4e47ea67b
kate
  Mon May 13 16:53:13 2019 -0700
Split tracks into .new.ra and .dev.ra to facilitate staging alpha, beta and not interfere with public tracks. refs #21139

diff --git src/hg/makeDb/doc/encode3/tfbs.txt src/hg/makeDb/doc/encode3/tfbs.txt
index 9b2a5fb..be450bf 100644
--- src/hg/makeDb/doc/encode3/tfbs.txt
+++ src/hg/makeDb/doc/encode3/tfbs.txt
@@ -367,30 +367,35 @@
 #       22Rv1 -> X22Rv1
 #       MM.1S -> MM_1S
 
 # rename tables (encode3Tfbs -> encTfChipPk)
 
 hgsql hg19 -e 'show tables like "encode3TfbsPk%"' > tables.old.txt
 sed -e 's/^/alter table /' -e 's/$/ rename to /' tables.old.txt > rename.1.sql
 sed -e 's/encode3TfbsPk/encTfChipPk/' tables.old.txt | paste rename.1.sql -  | \
     sed 's/$/;/' > rename.sql
 hgsql hg19 < rename.sql
 
 #  reload cluster input table
 hgLoadSqlTab hg19 encode3RegTfbsClusterInput \
         ~/kent/src/hg/lib/clusterInputTrackTable5.sql clusters.inputs.tab
 
+# rename field in cluster input table
+# NOTE syntax change in MariaDb (now requires type)
+hgsql -e hg19 "alter table encRegTfbsClusteredInputs change treatment experiment varchar(255)"
+
+
 ###############
 # hg38
 
 cd ../hg38
 mkdir scoredPeaks
 cd peaks
 awk '{print $1}' ../fileCellAbTarget.tab | sed 's/peaks\///' | \
         xargs -L 1 ../../scorePeaks.csh hg38 >&! ../scorePeaks.log &
 
 cd ..
 perl ../makeTrackDb.pl < clusters.inputs.tab > trackDb.ra
 
 paste cells.txt cells.txt > cellGroup.txt
 # edit for subgroup format
 
@@ -408,30 +413,34 @@
 #       22Rv1 -> X22Rv1
 #       MM.1S -> MM_1S
 
 # rename tables (encode3Tfbs -> encTfChipPk)
 
 hgsql hg38 -e 'show tables like "encode3TfbsPk%"' > tables.old.txt
 sed -e 's/^/alter table /' -e 's/$/ rename to /' tables.old.txt > rename.1.sql
 sed -e 's/encode3TfbsPk/encTfChipPk/' tables.old.txt | paste rename.1.sql -  | \       
     sed 's/$/;/' > rename.sql
 hgsql hg38 < rename.sql
 
 #  reload cluster input table
 hgLoadSqlTab hg38 encode3RegTfbsClusterInput \
         ~/kent/src/hg/lib/clusterInputTrackTable5.sql clusters.inputs.tab
 
+# rename field in cluster input table
+# NOTE syntax change in MariaDb (now requires type)
+hgsql -e hg19 "alter table encRegTfbsClusteredInputs change treatment experiment varchar(255)"
+
 ####################
 # Motifs (hg38) from Henry Pratt at Zlab
 # 2019-03-13
 
 # Notes from Henry:
 
 #The structure is mostly the same as the existing tables: canonical.tsv contains lists 
 # of canonical motifs for each factor, pwms.tsv contains the PWM list for the motifs, 
 # and fimo.tsv contains a large list of occurrences for each motif. We have expanded 
 # the number of canonical motifs in many cases to more than two, including some novel 
 # motifs MEME discovered which aren't annotated in the databases I searched. 
 # That's a primary area where we'll probably look to filter and/or merge PWMs to 
 # reduce the size a little bit more."
 
 cd /hive/data/outside/encode3/tfbs/dac