src/hg/makeDb/doc/mm9.txt 1.109

Index: src/hg/makeDb/doc/mm9.txt
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/doc/mm9.txt,v
retrieving revision 1.108
retrieving revision 1.109
diff -b -B -U 4 -r1.108 -r1.109
--- src/hg/makeDb/doc/mm9.txt	3 Sep 2009 15:39:32 -0000	1.108
+++ src/hg/makeDb/doc/mm9.txt	4 Sep 2009 16:52:27 -0000	1.109
@@ -9489,9 +9489,9 @@
    svn+ssh://hgwdev.cse.ucsc.edu/projects/compbio/usr/markd/svn/projs/transMap/tags/vertebrate.2009-07-01
 
 see doc/builds.txt for specific details.
 ############################################################################
-# VEGA GENES UPDATE TO BUILD 35 (DONE, 2009-07-30, hartera)
+# VEGA GENES UPDATE TO BUILD 35 (DONE, 2009-07-30 - 2009-09-04, hartera)
 # Needs updating as the current version is build 31 from May 2008.
 # 2009-08-03 (hartera) - Added code to register track handler for
 # vegaGeneComposite.
 # 2009-08-15 - 2009-08-16 (hartera) - Added code to allow use of radio buttons
@@ -9501,9 +9501,12 @@
 # 2009-08-22 - Finished code for adding Vega report URLs to the details pages.
 # Loaded the vegaGtp table.
 # 2009-09-01 and 2009-09-03 (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 -p /hive/data/genomes/mm9/bed/vega35
+   cd /hive/data/genomes/mm9/bed/vega35
    # Download the VEGA genes for mouse from the ftp site
    # This file is from 03/17/09.
    wget --timestamping \
         "ftp://ftp.sanger.ac.uk/pub/vega/mouse/gtf_file.gz"
@@ -9600,8 +9603,22 @@
    # in the type line for src/hg/makeDb/trackDb/mouse/mm9/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/mm9/bed/vega35
+   hgsql -e 'drop table vegaGene;' mm9
+   hgsql -e 'drop table vegaPseudoGene;' mm9
+   hgLoadGenePred -genePredExt mm9 vegaGene not.pseudo.gp
+   hgLoadGenePred -genePredExt mm9 vegaPseudoGene pseudo.gp
+   hgsql -e 'drop table vegaGtp;' mm9
+   hgLoadSqlTab mm9 vegaGtp ensGtp.sql vegaGtp.tab
+   hgsql -e 'drop table vegaPep;' mm9
+   hgPepPred mm9 tab vegaPep vegaPep.mm9.fa.tab
+
 ############################################################################
 # Blastz Elephant loxAfr3 (DONE - 2009-08-12 - Hiram)
     mkdir /hive/data/genomes/mm9/bed/lastzLoxAfr3.2009-08-12
     cd /hive/data/genomes/mm9/bed/lastzLoxAfr3.2009-08-12