5adcf6bc2904690de7b7b30a83ec8a7a0996abe9 galt Tue Aug 21 00:01:25 2018 -0700 changing cse subdomain to soe diff --git src/utils/qa/chain2.csh src/utils/qa/chain2.csh index 1c12c68..cdbee33 100755 --- src/utils/qa/chain2.csh +++ src/utils/qa/chain2.csh @@ -134,31 +134,31 @@ echo echo "*~*~*~*~*~*~*~*~*~*~*~*~*~*" echo echo "checking that all chroms (scaffolds) have chains in chain table" hgsql -N -e "SELECT DISTINCT(tName) FROM $track" $db | sort > $db.$track.chroms commTrio.csh $db.chromlist$$ $db.$track.chroms if ( `wc -l $db.chromlist$$.Only | awk '{print $1}'` > 0 ) then # some chroms have not chains. display links. # get multiz info for link set multiz=`hgsql -N -e "SHOW TABLES LIKE 'multiz%'" $db | head -1` echo "these have no chains:" if ( $multiz != "" ) then set multiz="&${multiz}=pack" endif foreach seq ( `head -3 $db.chromlist$$.Only` ) - echo "http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=$db&position=$seq&chain$Org=pack$multiz" + echo "http://genome-test.soe.ucsc.edu/cgi-bin/hgTracks?db=$db&position=$seq&chain$Org=pack$multiz" end echo "get some DNA from these and see how it blats on $otherDb" else echo "all chroms have chains" endif endif # ------------------------------------------------- # Link table: make list of uniq chainIds. # check if they all exist as chainOrg.id # dropped this. duplicates joinerCheck echo echo "*~*~*~*~*~*~*~*~*~*~*~*~*~*" echo "running joinerCheck"