4fdac1a09cb6a154a2f739885b02fc8f0e40a00d
hiram
  Mon Sep 9 09:57:59 2019 -0700
first instance of hub is complete refs #23734

diff --git src/hg/makeDb/doc/VGP/mkSymLinks.sh src/hg/makeDb/doc/VGP/mkSymLinks.sh
index 6581962..6430d46 100755
--- src/hg/makeDb/doc/VGP/mkSymLinks.sh
+++ src/hg/makeDb/doc/VGP/mkSymLinks.sh
@@ -1,29 +1,32 @@
 #!/bin/bash
 
 set -beEu -o pipefail
 
 cd /hive/data/genomes/asmHubs/VGP/ucscNames
 
 ls -d */bbi | sed -e 's#/bbi##;' | while read asmId
 do
    mkdir -p /gbdb/hubs/VGP/genomes/$asmId /gbdb/hubs/VGP/genomes/$asmId/html
    rm -f /gbdb/hubs/VGP/genomes/$asmId/bbi
    rm -f /gbdb/hubs/VGP/genomes/$asmId/ixIxx
    rm -f /gbdb/hubs/VGP/genomes/$asmId/html/*.html
    rm -f /gbdb/hubs/VGP/genomes/$asmId/html/*.jpg
    rm -f /gbdb/hubs/VGP/genomes/$asmId/html/*.png
    rm -f /gbdb/hubs/VGP/genomes/$asmId/$asmId.2bit
+   rm -f /gbdb/hubs/VGP/genomes/$asmId/$asmId.agp
+   rm -f /gbdb/hubs/VGP/genomes/$asmId/$asmId.agp.gz
    rm -f /gbdb/hubs/VGP/genomes/$asmId/$asmId.genomes.txt
    rm -f /gbdb/hubs/VGP/genomes/$asmId/$asmId.trackDb.txt
    rm -f /gbdb/hubs/VGP/genomes/$asmId/$asmId.chrom.sizes
    rm -f /gbdb/hubs/VGP/genomes/$asmId/${asmId}_assembly_report.txt
    ln -s `pwd -P`/$asmId/bbi /gbdb/hubs/VGP/genomes/$asmId/bbi
    ln -s `pwd -P`/$asmId/ixIxx /gbdb/hubs/VGP/genomes/$asmId/ixIxx
    ln -s `pwd -P`/$asmId/html/*.html /gbdb/hubs/VGP/genomes/$asmId/html/
    ln -s `pwd -P`/$asmId/html/*.jpg /gbdb/hubs/VGP/genomes/$asmId/html/
    ln -s `pwd -P`/$asmId/trackData/addMask/$asmId.masked.2bit /gbdb/hubs/VGP/genomes/$asmId/$asmId.2bit
+   ln -s `pwd -P`/$asmId/$asmId.agp.gz /gbdb/hubs/VGP/genomes/$asmId/$asmId.agp.gz
    ln -s `pwd -P`/$asmId/$asmId.genomes.txt /gbdb/hubs/VGP/genomes/$asmId
    ln -s `pwd -P`/$asmId/$asmId.chrom.sizes /gbdb/hubs/VGP/genomes/$asmId
    ln -s `pwd -P`/$asmId/$asmId.trackDb.txt /gbdb/hubs/VGP/genomes/$asmId
    ln -s `pwd -P`/$asmId/download/${asmId}_assembly_report.txt /gbdb/hubs/VGP/genomes/$asmId/
 done