68c790ea17562c97c9c0d54346446196a11cbd6d
hiram
  Thu Feb 23 11:38:13 2023 -0800
up to date with latest fixes no redmine

diff --git src/hg/utils/otto/grcIncident/grcUpdate.sh src/hg/utils/otto/grcIncident/grcUpdate.sh
index 6569345..be1e386 100755
--- src/hg/utils/otto/grcIncident/grcUpdate.sh
+++ src/hg/utils/otto/grcIncident/grcUpdate.sh
@@ -30,34 +30,42 @@
 if [ -s updateRunning.pid ]; then
   printf "To: $failMail\nFrom: $failMail\nSubject: ERROR: GRC Incident update $Db\n\nERROR: ${db} GRC incident update, previous update did not finish\n" | /usr/sbin/sendmail -t -oi
 
 #  echo "ERROR: ${db} GRC incident update, previous update did not finish" \
 #        | /bin/mail -s "ERROR: GRC Incident update $Db" ${failMail}
 #            > /dev/null 2> /dev/null
   exit 245
 fi
 
 echo $$ > updateRunning.pid
 
 export YM=`date "+%Y/%m"`
 mkdir -p ${YM}
 export DS=`date "+%F"`
 
+if [ $debug -ne 0 ]; then
+  printf "# %s\n" "https://ftp.ncbi.nlm.nih.gov/pub/grc/${ftpPath}" 1>&2
+  printf "# into ${YM}/${GRC_issue}.${DS}.gff\n" 1>&2
+fi
+
 wget --timestamping \
  https://ftp.ncbi.nlm.nih.gov/pub/grc/${ftpPath} \
    -O ${YM}/${GRC_issue}.${DS}.gff > /dev/null 2>&1
 gzip -f ${YM}/${GRC_issue}.${DS}.gff
+if [ $debug -ne 0 ]; then
+  ls -og ${YM}/${GRC_issue}.${DS}.gff.gz 1>&2
+fi
 
 if [ $debug -ne 0 ]; then
   printf "# fetched into ${workDir}/${YM}/${GRC_issue}.${DS}.gff\n" 1>&2
 fi
 
 if [ "${db}" = "mm9" ]; then
 /hive/data/outside/otto/grcIncidentDb/parseGff.pl \
   ${YM}/${GRC_issue}.${DS}.gff.gz | sort \
      |  join -t$'\t' validContigs - > ${YM}/${db}.${DS}.contigs.bed5
   /cluster/bin/x86_64/liftUp -type=.bed ${YM}/${db}.${DS}.bed5 refSeq.lift error ${YM}/${db}.${DS}.contigs.bed5
   gzip -f ${YM}/${db}.${DS}.contigs.bed5
 else
   /hive/data/outside/grc/incidentDb/parseGff.pl \
     ${YM}/${GRC_issue}.${DS}.gff.gz | sort \
      | join -t$'\t' refSeq.chromNames.tab - \
@@ -91,29 +99,30 @@
 if [ "${oldSum}" = "${newSum}" ]; then
 #    echo "${db} GRC update no change from previous ${DS}" \
 #         | mail -s "ALERT: GRC Incident update $Db" ${failMail} \
 #             > /dev/null 2> /dev/null
    rm -f ${YM}/${DS}.${Db}.grcIncidentDb.bb
    rm -f ${YM}/${db}.${DS}.bed5.gz
    rm -f ${YM}/${GRC_issue}.${DS}.gff.gz
    rm -f ${YM}/${db}.${DS}.contigs.bed5.gz
 else
    rm -f ${Db}.grcIncidentDb.bb
    cp -p ${YM}/${DS}.${Db}.grcIncidentDb.bb ${Db}.grcIncidentDb.bb
    printf "To: $failMail\nFrom: $failMail\nSubject: ALERT: GRC Incident update $Db\n\n=== Updated $Db ===\n%s\n" \
       "`${bbiInfo} -udcDir=./udcCache ${Db}.grcIncidentDb.bb`" \
 	| /usr/sbin/sendmail -t -oi
    rm -fr ./udcCache
-   /cluster/bin/scripts/gwUploadFile ${Db}.grcIncidentDb.bb ${Db}.grcIncidentDb.bb > /dev/null 2>&1
+# no longer necessary
+   # /cluster/bin/scripts/gwUploadFile ${Db}.grcIncidentDb.bb ${Db}.grcIncidentDb.bb > /dev/null 2>&1
    url=`/cluster/bin/x86_64/hgsql -N -e "select * from grcIncidentDb;" $db`
    rm -fr ./udcCache
    mkdir ./udcCache
    ${bbiInfo} -udcDir=./udcCache "${url}" 2>&1 \
         | mail -s "ALERT: GRC Incident update $Db" ${failMail} \
             > /dev/null 2> /dev/null
    rm -fr ./udcCache
    zcat ${YM}/${db}.${DS}.bed5.gz | cut -f4 | sort -u | awk '{printf "%s\t%s\n", $1, $1}' > ${Db}.nameIndex.txt
    /cluster/bin/x86_64/ixIxx ${Db}.nameIndex.txt ${Db}.grcIncidentDb.ix ${Db}.grcIncidentDb.ixx
 fi
 rm -f updateRunning.pid
 printf "SUCCESS\n"
 exit 0