ea79a1e6a7795f886789c87decc48cd89646fa2e
hiram
  Mon Jan 27 14:28:39 2020 -0800
destination directory for symlinks is now in a new location refs #24354

diff --git src/hg/makeDb/doc/globalReference/mkSymLinks.sh src/hg/makeDb/doc/globalReference/mkSymLinks.sh
index 002ca99..27ee40b 100755
--- src/hg/makeDb/doc/globalReference/mkSymLinks.sh
+++ src/hg/makeDb/doc/globalReference/mkSymLinks.sh
@@ -1,50 +1,51 @@
 #!/bin/bash
 
 set -beEu -o pipefail
 
 export Name="GlobalReference"
 export subDir="globalReference"
+export destDir="/usr/local/apache/htdocs-hgdownload/hubs"
 
 cd /hive/data/genomes/asmHubs/${subDir}
 
 ls -d */bbi | sed -e 's#/bbi##;' | while read asmId
 do
-   mkdir -p /gbdb/hubs/$subDir/genomes/$asmId /gbdb/hubs/$subDir/genomes/$asmId/html
-   rm -f /gbdb/hubs/$subDir/genomes/$asmId/bbi
-   rm -f /gbdb/hubs/$subDir/genomes/$asmId/ixIxx
-   rm -f /gbdb/hubs/$subDir/genomes/$asmId/html/*.html
-   rm -f /gbdb/hubs/$subDir/genomes/$asmId/$asmId.2bit
-   rm -f /gbdb/hubs/$subDir/genomes/$asmId/$asmId.agp
-   rm -f /gbdb/hubs/$subDir/genomes/$asmId/$asmId.agp.gz
-   rm -f /gbdb/hubs/$subDir/genomes/$asmId/$asmId.genomes.txt
-   rm -f /gbdb/hubs/$subDir/genomes/$asmId/$asmId.trackDb.txt
-   rm -f /gbdb/hubs/$subDir/genomes/$asmId/$asmId.chrom.sizes
-   rm -f /gbdb/hubs/$subDir/genomes/$asmId/${asmId}_assembly_report.txt
-   rm -f /gbdb/hubs/$subDir/hub.txt
-   rm -f /gbdb/hubs/$subDir/groups.txt
-   rm -f /gbdb/hubs/$subDir/index.html
-   rm -f /gbdb/hubs/$subDir/testIndex.html
-   rm -f /gbdb/hubs/$subDir/asmStats$Name.html
-   rm -f /gbdb/hubs/$subDir/testAsmStats$Name.html
-   rm -f /gbdb/hubs/$subDir/genomes.txt
-   ln -s `pwd -P`/$asmId/bbi /gbdb/hubs/$subDir/genomes/$asmId/bbi
-   ln -s `pwd -P`/$asmId/ixIxx /gbdb/hubs/$subDir/genomes/$asmId/ixIxx
-   ln -s `pwd -P`/$asmId/html/*.html /gbdb/hubs/$subDir/genomes/$asmId/html/
-   ln -s `pwd -P`/$asmId/trackData/addMask/$asmId.masked.2bit /gbdb/hubs/$subDir/genomes/$asmId/$asmId.2bit
-   ln -s `pwd -P`/$asmId/$asmId.agp.gz /gbdb/hubs/$subDir/genomes/$asmId/$asmId.agp.gz
-   ln -s `pwd -P`/$asmId/$asmId.genomes.txt /gbdb/hubs/$subDir/genomes/$asmId
-   ln -s `pwd -P`/$asmId/$asmId.chrom.sizes /gbdb/hubs/$subDir/genomes/$asmId
-   ln -s `pwd -P`/$asmId/$asmId.trackDb.txt /gbdb/hubs/$subDir/genomes/$asmId
-   ln -s `pwd -P`/$asmId/download/${asmId}_assembly_report.txt /gbdb/hubs/$subDir/genomes/$asmId/
-   ln -s /hive/data/genomes/asmHubs/${subDir}/hub.txt /gbdb/hubs/$subDir/
-   ln -s /hive/data/genomes/asmHubs/${subDir}/groups.txt /gbdb/hubs/$subDir/
-   ln -s /hive/data/genomes/asmHubs/${subDir}/index.html /gbdb/hubs/$subDir/
+   mkdir -p ${destDir}/$subDir/genomes/$asmId ${destDir}/$subDir/genomes/$asmId/html
+   rm -f ${destDir}/$subDir/genomes/$asmId/bbi
+   rm -f ${destDir}/$subDir/genomes/$asmId/ixIxx
+   rm -f ${destDir}/$subDir/genomes/$asmId/html/*.html
+   rm -f ${destDir}/$subDir/genomes/$asmId/$asmId.2bit
+   rm -f ${destDir}/$subDir/genomes/$asmId/$asmId.agp
+   rm -f ${destDir}/$subDir/genomes/$asmId/$asmId.agp.gz
+   rm -f ${destDir}/$subDir/genomes/$asmId/$asmId.genomes.txt
+   rm -f ${destDir}/$subDir/genomes/$asmId/$asmId.trackDb.txt
+   rm -f ${destDir}/$subDir/genomes/$asmId/$asmId.chrom.sizes
+   rm -f ${destDir}/$subDir/genomes/$asmId/${asmId}_assembly_report.txt
+   rm -f ${destDir}/$subDir/hub.txt
+   rm -f ${destDir}/$subDir/groups.txt
+   rm -f ${destDir}/$subDir/index.html
+   rm -f ${destDir}/$subDir/testIndex.html
+   rm -f ${destDir}/$subDir/asmStats$Name.html
+   rm -f ${destDir}/$subDir/testAsmStats$Name.html
+   rm -f ${destDir}/$subDir/genomes.txt
+   ln -s `pwd -P`/$asmId/bbi ${destDir}/$subDir/genomes/$asmId/bbi
+   ln -s `pwd -P`/$asmId/ixIxx ${destDir}/$subDir/genomes/$asmId/ixIxx
+   ln -s `pwd -P`/$asmId/html/*.html ${destDir}/$subDir/genomes/$asmId/html/
+   ln -s `pwd -P`/$asmId/trackData/addMask/$asmId.masked.2bit ${destDir}/$subDir/genomes/$asmId/$asmId.2bit
+   ln -s `pwd -P`/$asmId/$asmId.agp.gz ${destDir}/$subDir/genomes/$asmId/$asmId.agp.gz
+   ln -s `pwd -P`/$asmId/$asmId.genomes.txt ${destDir}/$subDir/genomes/$asmId
+   ln -s `pwd -P`/$asmId/$asmId.chrom.sizes ${destDir}/$subDir/genomes/$asmId
+   ln -s `pwd -P`/$asmId/$asmId.trackDb.txt ${destDir}/$subDir/genomes/$asmId
+   ln -s `pwd -P`/$asmId/download/${asmId}_assembly_report.txt ${destDir}/$subDir/genomes/$asmId/
+   ln -s /hive/data/genomes/asmHubs/${subDir}/hub.txt ${destDir}/$subDir/
+   ln -s /hive/data/genomes/asmHubs/${subDir}/groups.txt ${destDir}/$subDir/
+   ln -s /hive/data/genomes/asmHubs/${subDir}/index.html ${destDir}/$subDir/
    sed -e "s/hgdownload.soe/genome-test.gi/g; s/asmStats$Name/testAsmStats$Name/;" /hive/data/genomes/asmHubs/${subDir}/index.html > /hive/data/genomes/asmHubs/${subDir}/testIndex.html
    chmod +x /hive/data/genomes/asmHubs/${subDir}/testIndex.html
-   ln -s /hive/data/genomes/asmHubs/${subDir}/testIndex.html /gbdb/hubs/$subDir/
-   ln -s /hive/data/genomes/asmHubs/${subDir}/genomes.txt /gbdb/hubs/$subDir/
-   ln -s /hive/data/genomes/asmHubs/${subDir}/asmStats$Name.html /gbdb/hubs/$subDir/
+   ln -s /hive/data/genomes/asmHubs/${subDir}/testIndex.html ${destDir}/$subDir/
+   ln -s /hive/data/genomes/asmHubs/${subDir}/genomes.txt ${destDir}/$subDir/
+   ln -s /hive/data/genomes/asmHubs/${subDir}/asmStats$Name.html ${destDir}/$subDir/
    sed -e 's/hgdownload.soe/genome-test.gi/g; s/index.html/testIndex.html/;' /hive/data/genomes/asmHubs/${subDir}/asmStats$Name.html > /hive/data/genomes/asmHubs/${subDir}/testAsmStats$Name.html
    chmod +x /hive/data/genomes/asmHubs/${subDir}/testAsmStats$Name.html
-   ln -s /hive/data/genomes/asmHubs/${subDir}/testAsmStats$Name.html /gbdb/hubs/$subDir/
+   ln -s /hive/data/genomes/asmHubs/${subDir}/testAsmStats$Name.html ${destDir}/$subDir/
 done