f16809aeb7fd0420f7575692e352ca78054f4213
hiram
  Tue Jul 23 16:35:51 2024 -0700
scripts to make links for GenArk hubs into gbdb for potential copy to asia and euro nodes and dynamic blat backup directory refs #33526

diff --git src/hg/makeDb/doc/asmHubs/gbDbLinks.sh src/hg/makeDb/doc/asmHubs/gbDbLinks.sh
new file mode 100755
index 0000000..024239c
--- /dev/null
+++ src/hg/makeDb/doc/asmHubs/gbDbLinks.sh
@@ -0,0 +1,55 @@
+#!/bin/bash
+
+set -beEu -o pipefail
+
+if [ $# -lt 1 ]; then
+  printf "usage: gdDbLinks.sh asmId [... asmId ...]\n" 1>&2
+  exit 255
+fi
+
+for asmId in $*
+do
+  gcX="${asmId:0:3}"
+  d0="${asmId:4:3}"
+  d1="${asmId:7:3}"
+  d2="${asmId:10:3}"
+  acc=`echo $asmId | cut -d'_' -f1-2`
+  downDir="/hive/data/genomes/asmHubs/${gcX}/${d0}/${d1}/${d2}/${acc}"
+  dbDbDir="/gbdb/genark/${gcX}/${d0}/${d1}/${d2}/${acc}"
+  if [ ! -d "${dbDbDir}" ]; then
+    mkdir -p "${dbDbDir}"
+    mkdir -p "${dbDbDir}/html"
+    mkdir -p "${dbDbDir}/bbi"
+    mkdir -p "${dbDbDir}/ixIxx"
+  fi
+  for ext in 2bit 2bit.bpt chrom.sizes.txt chromAlias.bb
+  do
+    rm -f "${dbDbDir}/${acc}.${ext}"
+    ln -s "${downDir}/${acc}.${ext}" "${dbDbDir}/${acc}.${ext}"
+  done
+  for txt in hub groups
+  do
+    rm -f "${dbDbDir}/${txt}.txt"
+    ln -s "${downDir}/${txt}.txt" "${dbDbDir}/${txt}.txt"
+  done
+  # clear entirely the html directory
+  (ls ${dbDbDir}/html/*.html 2> /dev/null || true) | while read htmlFile
+  do
+     rm -f "${htmlFile}"
+  done
+  for htmlFile in ${downDir}/html/*.html
+  do
+    fileName=`basename $htmlFile`
+    ln -s "${htmlFile}" "${dbDbDir}/html/${fileName}"
+  done
+  # clear entirely the bbi directory
+  (ls ${dbDbDir}/bbi/*.bb ${dbDbDir}/bbi/*.bw 2> /dev/null || true) | while read bigFile
+  do
+     rm -f "${bigFile}"
+  done
+  for bigFile in ${downDir}/bbi/*.bb ${downDir}/bbi/*.bw
+  do
+    fileName=`basename $bigFile`
+    ln -s "${bigFile}" "${dbDbDir}/bbi/${fileName}"
+  done
+done