3a6f7a2ceb39e56238f5a5d3ffa8c40a6d39f14e
hiram
  Tue Aug 11 13:14:09 2026 -0700
better organization of the asmAlias update procedure refs #31811

diff --git src/hg/utils/otto/genArk/asmAlias/runUpdate.sh src/hg/utils/otto/genArk/asmAlias/runUpdate.sh
index ad9a6232021..2676b1e2b53 100755
--- src/hg/utils/otto/genArk/asmAlias/runUpdate.sh
+++ src/hg/utils/otto/genArk/asmAlias/runUpdate.sh
@@ -11,31 +11,31 @@
 export YMD Y M DS
 
 export db="hgcentraltest"
 export logDir="${TOP}/log/${Y}/${M}"
 mkdir -p "${logDir}"
 export logFile="${logDir}/${DS}.txt"
 export prevAliasTsv="${logDir}/${YMD}.asmAlias.tsv.gz"
 export updateTsv="${logDir}/update.${YMD}.tsv"
 
 # do not overwrite this copy if it was already done today
 if [ ! -s "${prevAliasTsv}" ]; then
   hgsql -N -e 'select * from asmAlias;' "${db}" \
     | gzip -c > "${prevAliasTsv}"
 fi
 
-printf "### cwd: %s\n" "`pwd -P`" >> "${logFile}"
+printf "### cwd: %s\n" "$(pwd -P)" >> "${logFile}"
 printf "### logFile: log/${Y}/${M}/${DS}.txt.gz\n" >> "${logFile}"
 printf "####### running the update command:\n" >> "${logFile}"
 printf "time (./asmAliasUpdate.py -o update.${YMD}.tsv > update.${DS}.out 2> update.${DS}.err) >> logFile\n" >> "${logFile}"
 
 time (./asmAliasUpdate.py -o "${updateTsv}" > ${logDir}/update.${DS}.out 2> ${logDir}/update.${DS}.err) >> "${logFile}" 2>&1
 
 # watch for any new types of errors
 unexpected=$(egrep -v "OBSOLETE|UPDATE|NEW ALIAS|NOTE" "${logDir}/update.${DS}.err" \
     | egrep -v "ing to browser=[a-z]" \
       | egrep -v "are not case-independent|skipping" \
         | grep ERROR || true)
 if [ -n "${unexpected}" ]; then
     printf '%s\n' "${unexpected}" 1>&2
     echo "unexpected ERROR lines found, aborting before load" 1>&2
     exit 1