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/dynaBlatLinks.sh src/hg/makeDb/doc/asmHubs/dynaBlatLinks.sh
new file mode 100755
index 0000000..4f83a7a
--- /dev/null
+++ src/hg/makeDb/doc/asmHubs/dynaBlatLinks.sh
@@ -0,0 +1,29 @@
+#!/bin/bash
+
+set -beEu -o pipefail
+
+if [ $# -lt 1 ]; then
+  printf "usage: gdDbLinks.sh asmId [... asmId ...]\n" 1>&2
+  exit 255
+fi
+
+export dynaBlatLinks="/hive/data/inside/dynaBlat/backUpLinks"
+
+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}"
+  linksDir="${dynaBlatLinks}/${gcX}/${d0}/${d1}/${d2}/${acc}"
+  if [ ! -d "${linksDir}" ]; then
+    mkdir -p "${linksDir}"
+  fi
+  for ext in 2bit trans.gfidx untrans.gfidx
+  do
+    rm -f "${linksDir}/${acc}.${ext}"
+    ln -s "${downDir}/${acc}.${ext}" "${linksDir}/${acc}.${ext}"
+  done
+done