src/hg/makeDb/doc/hg18.txt 1.380

Index: src/hg/makeDb/doc/hg18.txt
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/doc/hg18.txt,v
retrieving revision 1.379
retrieving revision 1.380
diff -b -B -U 4 -r1.379 -r1.380
--- src/hg/makeDb/doc/hg18.txt	3 Sep 2009 15:39:14 -0000	1.379
+++ src/hg/makeDb/doc/hg18.txt	4 Sep 2009 16:51:03 -0000	1.380
@@ -28615,9 +28615,9 @@
     # Converted stdin, upper limit 11.63, lower limit -28.64
     hgLoadWiggle -pathPrefix=/gbdb/hg18/wib hg18 sfrs1ConsensusSites sfrs1ConsensusSites.wig
     ln -s $(pwd -P)/sfrs1ConsensusSites.wib /gbdb/hg18/wib/
 ############################################################################
-# VEGA GENES UPDATE TO BUILD 35 (DONE, 2009-08-04, hartera)
+# VEGA GENES UPDATE TO BUILD 35 (DONE, 2009-08-04 - 2009-09-04, hartera)
 # Needs updating as the current version is build 33.
 # Download the human VEGA Genes posted on ftp site on 2009-03-31
 # 2009-08-03 (hartera) - Added code to register track handler for
 # vegaGeneComposite.
@@ -28628,8 +28628,10 @@
 # 2009-08-22 - Finished code for adding Vega report URLs to the details pages.
 # Loaded the vegaGtp table.
 # 2009-09-01 - 2009-09-02 (hartera). Loaded a vegaPep table for the protein
 # sequence link on the details pages.
+# 2009-08-04 Re-load all tables as some reverted to the older version during
+# mySQL 5 upgrade.
 
     mkdir /hive/data/genomes/hg18/bed/vega35
     cd /hive/data/genomes/hg18/bed/vega35
     wget --timestamping "ftp://ftp.sanger.ac.uk/pub/vega/human/*" \
@@ -28718,5 +28720,18 @@
     # Add vegaPep to the trackDb.ra entry for the vegaGeneComposite track 
     # in the type line for src/hg/makeDb/trackDb/human/hg18/trackDb.ra.
     # Check that the vegaPep table looks ok and then check protein-coding and 
     # noncoding transcript details pages for protein links.
+    # 2009-09-04, hartera
+    # Re-load tables after upgrade to mySQL 5 as they had reverted back to 
+    # tables with the previous Vega dataset.
+    
+    cd /hive/data/genomes/hg18/bed/vega35
+    hgsql -e 'drop table vegaGene;' hg18
+    hgsql -e 'drop table vegaPseudoGene;' hg18
+    hgLoadGenePred -genePredExt hg18 vegaGene not.pseudo.gp
+    hgLoadGenePred -genePredExt hg18 vegaPseudoGene pseudo.gp
+    hgsql -e 'drop table vegaGtp;' hg18
+    hgLoadSqlTab hg18 vegaGtp ensGtp.sql vegaGtp.tab
+    hgsql -e 'drop table vegaPep;' hg18
+    hgPepPred hg18 tab vegaPep vegaPep.hg18.fa.tab
 ############################################################################