src/utils/qa/getAssemblies.csh 1.23
1.23 2010/01/22 21:17:19 kuhn
fixed getAssemblies.csh to work with RR machines and several other programs that it depends on. it broke when we went to a single mysql machine and genbank dumps only grab from hgnfs1
Index: src/utils/qa/getAssemblies.csh
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/utils/qa/getAssemblies.csh,v
retrieving revision 1.22
retrieving revision 1.23
diff -b -B -U 4 -r1.22 -r1.23
--- src/utils/qa/getAssemblies.csh 13 Apr 2009 19:38:19 -0000 1.22
+++ src/utils/qa/getAssemblies.csh 22 Jan 2010 21:17:19 -0000 1.23
@@ -16,8 +16,11 @@
set rr="false"
set dumpDate=""
set quiet=1
+set debug=true
+set debug=false
+
if ( "$HOST" != "hgwdev" ) then
echo "\n error: you must run this script on dev!\n"
exit 1
endif
@@ -35,14 +38,11 @@
else
set tablename=$argv[1]
endif
-set debug=0
-
# assign command line arguments
-set argNum=$#argv
-if ( $argv[$argNum] == "verbose" ) then
+if ( $argv[$#argv] == "verbose" ) then
set quiet=0
endif
if (($#argv > 1 && $quiet == 1) || $#argv == 3 ) then
@@ -53,23 +53,10 @@
else
endif
-if ($debug == 1) then
- echo "tablename = $tablename"
- echo "machine = $machine"
- echo "host = $host"
- echo "found = $found"
- echo "dbs = $dbs"
- echo "rr = $rr"
- echo "quiet = $quiet"
- echo "dumpDate = $dumpDate"
- echo
-endif
-
# check machine validity
checkMachineName.csh $machine
-
if ( $status ) then
echo "${0}:"
$0
exit 1
@@ -83,17 +71,28 @@
else
set host=""
set dumpDate=`getRRdatabases.csh $machine | grep "last dump" \
| gawk '{print $NF}'`
- set dbs=`getRRdatabases.csh $machine | grep -v "last dump"`
- set checkMach=`echo $dbs | grep "is not a valid"`
+ set dbs=`getRRdatabases.csh $machine | egrep -v "inform|last dump"`
+ echo $dbs | grep "is not a valid" > /dev/null
if ( $status == 0 ) then
- echo " $dbs"
echo
exit 1
endif
endif
+if ( $debug == "true" ) then
+ echo "tablename = $tablename"
+ echo "machine = $machine"
+ echo "host = $host"
+ echo "found = $found"
+ echo "dbs = $dbs"
+ echo "rr = $rr"
+ echo "quiet = $quiet"
+ echo "dumpDate = $dumpDate"
+ echo
+endif
+
# -------------------------------------------------
# get all assemblies containing $tablename
echo
@@ -140,12 +139,13 @@
if ( $quiet == 0 ) then
echo "checking "$db
endif
# check for chromInfo table on dev
- set isChromInfo=1
hgsql -N $host -e 'SHOW TABLES' $db | grep "chromInfo" > /dev/null
if ( $status ) then
set isChromInfo=0
+ else
+ set isChromInfo=1
endif
if ( $isChromInfo == 1 ) then
set chrom=`hgsql -N $host -e 'SELECT chrom FROM chromInfo LIMIT 1' $db`
# check if split table (on dev)