10a6e5cd8350a3409c7a053ac6f78be70f459c2c
hiram
  Mon Oct 7 14:20:32 2019 -0700
files to build the platinum genomes assembly hub refs #21784

diff --git src/hg/makeDb/doc/platinum/mkSymLinks.sh src/hg/makeDb/doc/platinum/mkSymLinks.sh
new file mode 100755
index 0000000..7a8eeb3
--- /dev/null
+++ src/hg/makeDb/doc/platinum/mkSymLinks.sh
@@ -0,0 +1,52 @@
+#!/bin/bash
+
+set -beEu -o pipefail
+
+export subDir="platinum"
+
+cd /hive/data/genomes/asmHubs/${subDir}Genomes
+
+ls -d */bbi | sed -e 's#/bbi##;' | while read asmId
+do
+   mkdir -p /gbdb/hubs/$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/$asmId/html/*.jpg
+   rm -f /gbdb/hubs/$subDir/genomes/$asmId/html/*.png
+   rm -f /gbdb/hubs/$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/$subDir/asmStatsPlatinum.html
+   rm -f /gbdb/hubs/$subDir/testAsmStatsPlatinum.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`/$asmId/html/*.jpg /gbdb/hubs/$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}Genomes/hub.txt /gbdb/hubs/$subDir/
+   ln -s /hive/data/genomes/asmHubs/${subDir}Genomes/groups.txt /gbdb/hubs/$subDir/
+   ln -s /hive/data/genomes/asmHubs/${subDir}Genomes/index.html /gbdb/hubs/$subDir/
+   sed -e 's/hgdownload.soe/genome-test.gi/g; s/asmStatsPlatinum/testAsmStatsPlatinum/;' /hive/data/genomes/asmHubs/${subDir}Genomes/index.html > /hive/data/genomes/asmHubs/${subDir}Genomes/testIndex.html
+   chmod +x /hive/data/genomes/asmHubs/${subDir}Genomes/testIndex.html
+   ln -s /hive/data/genomes/asmHubs/${subDir}Genomes/testIndex.html /gbdb/hubs/$subDir/
+   ln -s /hive/data/genomes/asmHubs/${subDir}Genomes/genomes.txt /gbdb/hubs/$subDir/
+   ln -s /hive/data/genomes/asmHubs/${subDir}Genomes/asmStatsPlatinum.html /gbdb/hubs/$subDir/
+   sed -e 's/hgdownload.soe/genome-test.gi/g; s/index.html/testIndex.html/;' /hive/data/genomes/asmHubs/${subDir}Genomes/asmStatsPlatinum.html > /hive/data/genomes/asmHubs/${subDir}Genomes/testAsmStatsPlatinum.html
+   chmod +x /hive/data/genomes/asmHubs/${subDir}Genomes/testAsmStatsPlatinum.html
+   ln -s /hive/data/genomes/asmHubs/${subDir}Genomes/testAsmStatsPlatinum.html /gbdb/hubs/$subDir/
+done