bedc0fc4c072a0a530a9556a9d00fdd1d43286ed
hiram
  Tue Feb 1 20:04:30 2022 -0800
verify there are gfidx files to go before trying that no redmine

diff --git src/hg/makeDb/doc/asmHubs/sendToHgdownload.sh src/hg/makeDb/doc/asmHubs/sendToHgdownload.sh
index aa312aa..916ad7f 100755
--- src/hg/makeDb/doc/asmHubs/sendToHgdownload.sh
+++ src/hg/makeDb/doc/asmHubs/sendToHgdownload.sh
@@ -1,61 +1,70 @@
 #!/bin/bash
 
 set -beEu -o pipefail
 
 if [ $# -ne 1 ]; then
   printf "usage: ./sendToHgdownload.sh <GCF/012/345/678/GCF_012345678.nn>\n" 1>&2
   exit 255
 fi
 
 export dirPath="${1}"
 
 ## verify no broken symlinks
 export srcDir="/hive/data/genomes/asmHubs/${dirPath}"
 
 badLinks=`(find "${srcDir}" -type l -lname \* \
   | xargs --no-run-if-empty ls -lL > /dev/null || true) 2>&1 | wc -l`
 
 ### printf "# badLinks: %s\n" "${badLinks}"
 
 if [ "${badLinks}" -gt 0 ]; then
   printf "ERROR: missing symlink targets:\n" 1>&2
   find "/hive/data/genomes/asmHubs/${dirPath}" -type l -lname \* \
     | xargs --no-run-if-empty ls -lL > /dev/null
   exit 255
 fi
 
 export destDir="/mirrordata/hubs/${dirPath}"
 printf "# srcDir: %s\n" "${srcDir}"
 printf "# destDir: %s\n" "${destDir}"
 
 ssh qateam@hgdownload.soe.ucsc.edu "mkdir -p ${destDir}" 2>&1 | grep -v "X11 forwarding request" || true
 printf "# successful mkdir on hgdownload\n"
 
 ### 2021-12-20 - out of disk space on dynablat
 
 if [ 1 -eq 0 ]; then
 
+### check if there are actually index files to go:
+
+export idxCount=`ls ${srcDir}/*.gfidx 2> /dev/null | wc -l`
+
+if [ "${idxCount}" -gt 0 ]; then
+
 export dynaServerDir="/scratch/hubs/${dirPath}"
 
 ssh qateam@dynablat-01.soe.ucsc.edu "mkdir -p ${dynaServerDir}" 2>&1 | grep -v "X11 forwarding request" || true
 printf "# successful mkdir on dynablat-01\n"
 
 rsync --stats -a -L -P ${srcDir}/*.2bit "qateam@dynablat-01.soe.ucsc.edu:${dynaServerDir}/" \
   2>&1 | grep -v "X11 forwarding request" || true
 rsync --stats -a -L -P ${srcDir}/*.gfidx "qateam@dynablat-01.soe.ucsc.edu:${dynaServerDir}/" \
   2>&1 | grep -v "X11 forwarding request" || true
 
 fi
+
+fi
+
 ### 2021-12-20 - out of disk space on dynablat
 ##################################################################
 
 # the new single file hub genome trackDb file:
 # genomes.txt obsolete now with the single file
 # ssh qateam@hgdownload.soe.ucsc.edu "rm ${destDir}/genomes.txt" 2>&1 | egrep -v "cannot remove|X11 forwarding request" || true
 # ssh qateam@hgdownload.soe.ucsc.edu "rm ${destDir}/html/*.description.html" 2>&1 | grep -v "X11 forwarding request" || true
 rsync --delete --exclude="hub.txt" --exclude="download.hub.txt" --stats -a -L -P "${srcDir}/" "qateam@hgdownload.soe.ucsc.edu:${destDir}/" \
   2>&1 | grep -v "X11 forwarding request" || true
 # the new single file hub genome trackDb file:
 rsync --stats -a -L -P "${srcDir}/download.hub.txt" "qateam@hgdownload.soe.ucsc.edu:${destDir}/hub.txt" \
   2>&1 | grep -v "X11 forwarding request" || true
 printf "# successful rsync\n"