e6b91e6964b0ba95a981e3991cde646cfbf68536
hiram
  Tue Mar 2 11:11:02 2021 -0800
browser is completed and pushed to RR refs #24074

diff --git src/hg/makeDb/doc/calJac4/initialBuild.txt src/hg/makeDb/doc/calJac4/initialBuild.txt
index 6944e16..bc084a5 100644
--- src/hg/makeDb/doc/calJac4/initialBuild.txt
+++ src/hg/makeDb/doc/calJac4/initialBuild.txt
@@ -1214,64 +1214,82 @@
 # liftOver to previous versions: 1, from previous versions: 1
 
     # fixup all.joiner until this is a clean output
     joinerCheck -database=calJac4 -tableCoverage all.joiner
     joinerCheck -database=calJac4 -times all.joiner
     joinerCheck -database=calJac4 -keys all.joiner
 
     # when clean, check in:
     git commit -m 'adding rules for calJac4 refs #24074' all.joiner
     git push
     # run up a 'make alpha' in hg/hgTables to get this all.joiner file
     # into the hgwdev/genome-test system
 
     cd /hive/data/genomes/calJac4
     time (makeDownloads.pl calJac4) > downloads.log 2>&1
-    #  real    16m11.233s
+    #  real    20m11.930s
 
     #   now ready for pushQ entry
     mkdir /hive/data/genomes/calJac4/pushQ
     cd /hive/data/genomes/calJac4/pushQ
  time ($HOME/kent/src/hg/utils/automation/makePushQSql.pl -redmineList calJac4) > calJac4.pushQ.sql 2> stderr.out
-    # real    15m2.385s
+    # real    13m21.313s
 
     # remove the tandemDups and gapOverlap from the file list:
     sed -i -e "/tandemDups/d" redmine.calJac4.table.list
     sed -i -e "/Tandem Dups/d" redmine.calJac4.releaseLog.txt
     sed -i -e "/gapOverlap/d" redmine.calJac4.table.list
     sed -i -e "/Gap Overlaps/d" redmine.calJac4.releaseLog.txt
 
+    # remove the multiz7way tables:
+    sed -i -e "/multiz7way/d" redmine.calJac4.table.list
+
+    # edit the file list and expand the wildcards: .../calJac*/...
+
     #   check for errors in stderr.out, some are OK, e.g.:
-  # WARNING: calJac4 does not have ucscToRefSeq
-  # WARNING: hgwdev does not have /gbdb/calJac4/ncbiRefSeq/ncbiRefSeqVersion.txt
-  # WARNING: hgwdev does not have /gbdb/calJac4/ncbiRefSeq/ncbiRefSeqOther.bb
-  # WARNING: hgwdev does not have /gbdb/calJac4/ncbiRefSeq/ncbiRefSeqOther.ix
-  # WARNING: hgwdev does not have /gbdb/calJac4/ncbiRefSeq/ncbiRefSeqOther.ixx
-  # WARNING: hgwdev does not have /gbdb/calJac4/ncbiRefSeq/seqNcbiRefSeq.rna.fa
-  # WARNING: calJac4 does not have seq
-  # WARNING: calJac4 does not have extFile
+# redmine.calJac4.releaseLog.txt
+WARNING: calJac4 does not have seq
+WARNING: hgwdev does not have phyloPng-generated /usr/local/apache/htdocs/images/phylo/calJac4_7way.gif (or png) for multiz7way.
+
+WARNING: Could not tell (from trackDb, all.joiner and hardcoded lists of
+supporting and genbank tables) which tracks to assign these tables to:
+  chainRBestHg38
+  chainRBestHg38Link
+  chainRBestMacFas5
+  chainRBestMacFas5Link
+... etc
+    crisprAllRanges
+  gbLoaded
+  netRBestHg38
+  netRBestMacFas5
+  netRBestMm10
+  netRBestMm39
+  netSynHg38
+  netSynMacFas5
+  netSynMm10
+  netSynMm39
 
     # verify the file list does correctly match to files
     cat redmine.calJac4.file.list | while read L
 do
   eval ls $L > /dev/null
 done
     # should be silent, missing files will show as errors
 
     # verify database tables, how many to expect:
     wc -l redmine.calJac4.table.list
-    # 52 redmine.calJac4.table.list
+    # 70 redmine.calJac4.table.list
 
     # how many actual:
     awk -F'.' '{printf "hgsql -N %s -e '"'"'show table status like \"%s\";'"'"'\n", $1, $2}' redmine.calJac4.table.list | sh | wc -l
-    # 52
+    # 70
 
     # would be a smaller number actual if some were missing
 
     # add the path names to the listing files in the redmine issue
     # in the three appropriate entry boxes:
 
 #	/hive/data/genomes/calJac4/pushQ/redmine.calJac4.file.list
 #	/hive/data/genomes/calJac4/pushQ/redmine.calJac4.releaseLog.txt
 #	/hive/data/genomes/calJac4/pushQ/redmine.calJac4.table.list
 
 #########################################################################