src/utils/qa/getGbdbBeta.csh 1.6

Index: src/utils/qa/getGbdbBeta.csh
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/utils/qa/getGbdbBeta.csh,v
retrieving revision 1.5
retrieving revision 1.6
diff -b -B -U 1000000 -r1.5 -r1.6
--- src/utils/qa/getGbdbBeta.csh	21 Mar 2009 00:29:25 -0000	1.5
+++ src/utils/qa/getGbdbBeta.csh	24 Mar 2009 19:10:44 -0000	1.6
@@ -1,109 +1,109 @@
 #!/bin/tcsh
 
 ####################
 #  06-20-05 Robert Kuhn
 #
 #  Script to dump /gbdb files from beta
 #
 ####################
 
 set filePath=""
 set db=""
 set todayDate=`date +%Y%m%d`
 
 if ($#argv != 1) then
   echo
   echo "  script to dump most /gbdb files from beta."
   echo "    gets all assembly files except ci1 and zoo."
   echo "    uses list of assemblies on beta."
   echo "       also list hgFixed."
   echo "    ignores files with Scaffold in the name "
   echo "       unless a db that uses them is specified."
   echo "    ignores: axtNetDp1, ci1, zoo, /sacCer1/sam."
   echo
   echo '      usage:  database or path (will use "all")'
   echo
   exit
 else
   set filePath=$argv[1]
   set outpath=`echo $filePath | sed -e 's/\//./'`
   set      db=`echo $filePath | sed -e 's/\/.*//'`
 endif
 
 set output=$outpath.gbdb.out
 set output2=$outpath.gbdb.list
   # echo "filePath = $filePath"
   # echo "outpath  = $outpath"
   # echo "db       = $db"
   # echo "output   = $output"
   # echo "output2  = $output2"
 
 rm -f $output
 rm -f $output2
 
 # get assembly list from beta
-hgsql -h hgofbeta -N -e "SELECT name FROM dbDb" hgcentralbeta \
+hgsql -h hgwbeta -N -e "SELECT name FROM dbDb" hgcentralbeta \
    | sort | grep -v ci1 | grep -v zoo > xxAssembliesxx
 echo "all" >> xxAssembliesxx
 echo "genbank" >> xxAssembliesxx
 echo "hgFixed" >> xxAssembliesxx
 
 # error checking for db name on command line
 # flag set to 1 if $db is actually an assembly (or genbank, all or hgFixed)"
 set dbFlag=0
 foreach assembly (`cat xxAssembliesxx`)
   # echo $assembly
   if ($db == "$assembly") then
     set dbFlag=1
     break
   endif
 end
 
 if ($dbFlag == "0") then
   echo '\n  '$db' is not an active assembly. try another assembly name, or "all"'
   echo
   exit
 endif
 
 # get the files from beta
 rm -f xxfullListxx
 if ($db == "all") then
   foreach assembly (`cat xxAssembliesxx | grep -v "all"`)
     # do not check Kevin's voluminous /sacCer1/sam/* files:
     if ( $assembly == "sacCer1" ) then
       set yeDirs=`ssh hgwbeta ls /gbdb/$assembly | grep -wv sam`
       foreach yedir ( $yeDirs )
         ssh hgwbeta find /gbdb/$assembly/$yedir -type f -print \
           | grep -vi Scaffold \
           | grep -v axtNetDp1   | grep -v "sacCer1/sam/" > tempfile
           # grep -v description | grep -v genbank \
         cat tempfile >> xxfullListxx
         cat tempfile
         rm -f tempfile
       end
     else 
       ssh hgwbeta find /gbdb/$assembly -type f -print | grep -vi Scaffold \
          | grep -v axtNetDp1   | grep -v "sacCer1/sam/" > tempfile
          # grep -v description | grep -v genbank \
       cat tempfile >> xxfullListxx
       cat tempfile
       rm -f tempfile
     endif
   end
 else
   if (-e /gbdb/$filePath) then
     ssh hgwbeta find /gbdb/$filePath -type f -print \
          | grep -v axtNetDp1   | grep -v "sacCer1/sam/" \
          | grep -v description > xxfullListxx
   else
     echo "\n  directory /gbdb/$filePath does not exist\n"
     exit
   endif
 endif
 
 sort xxfullListxx > gbdb.$db.$todayDate
 cp gbdb.$db.$todayDate /usr/local/apache/htdocs/qa/test-results/gbdb
 
 # clean up
 rm -f xxAssembliesxx
 rm -f xxfullListxx