404562a0949bf43b853017fa20a6fc70d22d4ccc
hiram
  Thu Feb 16 11:43:56 2023 -0800
update to GenArk hubs per user requests refs #29545

diff --git src/hg/makeDb/doc/asmHubs/sendToHgdownload.sh src/hg/makeDb/doc/asmHubs/sendToHgdownload.sh
index c4b2fca..ce3df87 100755
--- src/hg/makeDb/doc/asmHubs/sendToHgdownload.sh
+++ src/hg/makeDb/doc/asmHubs/sendToHgdownload.sh
@@ -1,68 +1,74 @@
 #!/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 DS=`date "+%F %T"`
 export destDir="/mirrordata/hubs/${dirPath}"
+printf "### sending %s\t%s\t##########\n" "`basename ${srcDir}`" "${DS}"
 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-01
 ### 2022-06-01 new dynamic-01 machine more disk space
 
 export dynaBlat="dynablat-01.soe.ucsc.edu"
 
 # export dynaBlat="128.114.119.136"
 
 ### 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 "mkdir -p ${dynaServerDir}" 2>&1 | grep -v "X11 forwarding request" || true
-printf "# successful mkdir on $dynaBlat\n"
+printf "# successful mkdir on $dynaBlat\n" 1>&2
 
+printf "rsync --stats -a -L -P ${srcDir}/*.2bit \"qateam@$dynaBlat:${dynaServerDir}/\"\n" 1>&2
 rsync --stats -a -L -P ${srcDir}/*.2bit "qateam@$dynaBlat:${dynaServerDir}/" \
-  2>&1 | grep -v "X11 forwarding request" || true
+  2>&1 | grep -v "X11 forwarding request"
+printf "rsync --stats -a -L -P ${srcDir}/*.gfidx \"qateam@$dynaBlat:${dynaServerDir}/\"\n" 1>&2
 rsync --stats -a -L -P ${srcDir}/*.gfidx "qateam@$dynaBlat:${dynaServerDir}/" \
-  2>&1 | grep -v "X11 forwarding request" || true
+  2>&1 | grep -v "X11 forwarding request"
 
 fi
 
 # 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 ${destDir}/html/*.description.html" 2>&1 | grep -v "X11 forwarding request" || true
+printf "rsync --delete --exclude=\"hub.txt\" --exclude=\"download.hub.txt\" --stats -a -L -P \"${srcDir}/\" \"qateam@hgdownload.soe.ucsc.edu:${destDir}/\"\n" 1>&2
 rsync --delete --exclude="hub.txt" --exclude="download.hub.txt" --stats -a -L -P "${srcDir}/" "qateam@hgdownload.soe.ucsc.edu:${destDir}/" \
-  2>&1 | grep -v "X11 forwarding request" || true
+  2>&1 | grep -v "X11 forwarding request"
 # the new single file hub genome trackDb file:
+printf "rsync --stats -a -L -P \"${srcDir}/download.hub.txt\" \"qateam@hgdownload.soe.ucsc.edu:${destDir}/hub.txt\"\n" 1>&2
 rsync --stats -a -L -P "${srcDir}/download.hub.txt" "qateam@hgdownload.soe.ucsc.edu:${destDir}/hub.txt" \
-  2>&1 | grep -v "X11 forwarding request" || true
+  2>&1 | grep -v "X11 forwarding request"
 printf "# successful rsync\n"