d7d97045f093f991875b4bf0efd35d4b928e2967
hiram
  Mon Jul 29 18:10:16 2019 -0700
scripts used to build the VGP assembly hubs refs #23734

diff --git src/hg/makeDb/doc/VGP/mkSymLinks.sh src/hg/makeDb/doc/VGP/mkSymLinks.sh
new file mode 100755
index 0000000..bfbef3a
--- /dev/null
+++ src/hg/makeDb/doc/VGP/mkSymLinks.sh
@@ -0,0 +1,21 @@
+#!/bin/bash
+
+ls -d */bbi | sed -e 's#/bbi##;' | while read asmId
+do
+   mkdir -p /gbdb/hubs/VGP/genomes/$asmId
+   rm -f /gbdb/hubs/VGP/genomes/$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/$asmId/html
+   ln -s `pwd -P`/$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
+done