3837053174a8f39a555150e38d8763ef25309c90
chmalee
  Wed Apr 19 16:24:35 2017 -0700
Modifying joiner batch scripts so non soe emails still receive notifications that the scripts are done, no refs

diff --git src/utils/qa/joinerBatchTimes.csh src/utils/qa/joinerBatchTimes.csh
index 8a1cdc0..f35dd39 100755
--- src/utils/qa/joinerBatchTimes.csh
+++ src/utils/qa/joinerBatchTimes.csh
@@ -1,79 +1,79 @@
 #!/bin/tcsh 
 
 ##############################
 #
 # does joinerCheck -times for a set a databases at a time
 #
 ##############################
 
 set dbs = ''
 set active = ''
 set thisRun = ''
 
 # usage statement
 if ($#argv < 1 || $#argv > 2) then
   echo
   echo "  Does a batch run of joinerCheck -times"
   echo "  Choose one of three sets of databases:"
   echo "       all human assemblies [hg]"
   echo "       all mouse and rat assemblies [mm_rn]"
   echo "       all other assemblies [other]"
   echo "       'extra' databases (e.g. go and proteins) [extra]"
   echo
   echo "  usage: hg | mm_rn | other | extra"
   echo
   exit 1
 else
   set dbs = $argv[1]
 endif
 
 # make sure they made a good database choice
 if ($dbs != 'hg' && $dbs != 'mm_rn' && $dbs != 'other' && $dbs != 'extra') then
   echo
   echo "  I didn't understand your database choice."
   echo "  Choose between human [hg], mouse and rat [mm_rn],"
   echo "  all others [other], or extra databases (e.g. proteins) [extra]"
   echo
   exit 1
 endif
 
 set d = `date -u +%F`
 
 # make a file for the output
 set log = "batchTimes.$dbs.$d.log"
 
 echo "Batch joinerCheck run (-times) for $dbs databases" >> $log
 echo "Full reports in run dir `pwd`\n" >> $log
 echo "Start All `date`\n" >> $log
 
 # get the list of active databases on the RR
 set active=`getRRdatabases.csh hgw1 | grep -v "last dump"`
 
 # grep out of the $active list, the ones that they want to check during this run
 if ($dbs == 'hg') then
   set thisRun=`echo  $active | sed -e "s/ /\n/g" | grep '^hg'`
 endif
 
 if ($dbs == 'mm_rn') then
   set thisRun=`echo  $active | sed -e "s/ /\n/g" | grep '^mm\|^rn'`
 endif
 
 if ($dbs == 'other') then
   set thisRun=`echo  $active | sed -e "s/ /\n/g" | grep -v '^hg\|^mm\|^rn\|^sp\|^go\|^prot\|^visi\|^uni\|^lost'`
 endif
 
 if ($dbs == 'extra') then
   set thisRun=`echo  $active | sed -e "s/ /\n/g" | grep '^sp\|^go\|^prot\|^visi\|^uni'`
 endif
 
 # now do it!
 foreach db ($thisRun)
  echo "\nStart $db `date`" >> $log
     joinerCheck ~/kent/src/hg/makeDb/schema/all.joiner -database=$db -times >& $db.$d
  echo "End $db `date`" >> $log
 end
 
 echo "\n\nEnd All `date`" >> $log
 
-mail -s "$log results" $USER@soe.ucsc.edu < $log
+mail -s "$log results" $USER@ucsc.edu < $log