d84a661a8c877c41a109a21ba4f095d0f26c12c4
hiram
  Wed Jul 31 18:51:28 2019 -0700
add assembly report and run during the make refs #23734

diff --git src/hg/makeDb/doc/VGP/mkSymLinks.sh src/hg/makeDb/doc/VGP/mkSymLinks.sh
index bfbef3a..52c2704 100755
--- src/hg/makeDb/doc/VGP/mkSymLinks.sh
+++ src/hg/makeDb/doc/VGP/mkSymLinks.sh
@@ -1,21 +1,26 @@
 #!/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/$asmId
+   mkdir -p /gbdb/hubs/VGP/genomes/$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/$asmId/$asmId.2bit
    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
-   ln -s `pwd -P`/$asmId/bbi -f /gbdb/hubs/VGP/genomes/$asmId/bbi
-   ln -s `pwd -P`/$asmId/ixIxx -f /gbdb/hubs/VGP/genomes/$asmId/ixIxx
-   mkdir -p /gbdb/hubs/VGP/genomes/$asmId/html
+   rm -f /gbdb/hubs/VGP/genomes/$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/trackData/addMask/$asmId.masked.2bit /gbdb/hubs/VGP/genomes/$asmId/$asmId.2bit
    ln -s `pwd -P`/$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