bd6c1a5bfa64bdeea75e21d6863cd785c9e17107
hiram
  Tue Oct 1 13:56:26 2024 -0700
genome-source has now become githubusercontent refs #34449

diff --git src/hg/utils/automation/doRecipBest.pl src/hg/utils/automation/doRecipBest.pl
index 57dbf61..2f2fce4 100755
--- src/hg/utils/automation/doRecipBest.pl
+++ src/hg/utils/automation/doRecipBest.pl
@@ -263,32 +263,32 @@
 md5sum *.axt.gz > md5sum.txt
 _EOF_
     );
     if ($opt_trackHub) {
       $bossScript->add(<<_EOF_
 mkdir -p ../bigMaf
 cd ../bigMaf
 ln -s ../mafRBestNet/$tDb.$qDb.rbest.maf.gz ./$tDb.$qDb.rbestNet.maf.gz
 _EOF_
       );
     }
   }
   if ($opt_trackHub) {
       $bossScript->add(<<_EOF_
 cd $buildDir/bigMaf
-wget --no-check-certificate -O bigMaf.as 'http://genome-source.soe.ucsc.edu/gitlist/kent.git/raw/master/src/hg/lib/bigMaf.as'
-wget --no-check-certificate -O mafSummary.as 'http://genome-source.soe.ucsc.edu/gitlist/kent.git/raw/master/src/hg/lib/mafSummary.as'
+wget --no-check-certificate -O bigMaf.as 'https://raw.githubusercontent.com/ucscGenomeBrowser/kent/refs/heads/master/src/hg/lib/bigMaf.as'
+wget --no-check-certificate -O mafSummary.as 'https://raw.githubusercontent.com/ucscGenomeBrowser/kent/refs/heads/master/src/hg/lib/mafSummary.as'
 mafToBigMaf $tDb $tDb.$qDb.rbestNet.maf.gz stdout \\
   | sort -k1,1 -k2,2n > $tDb.$qDb.rbestNet.txt
 bedToBigBed -itemsPerSlot=4 -type=bed3+1 -as=bigMaf.as -tab  $tDb.$qDb.rbestNet.txt \\
   $targetSizes $tDb.$qDb.rbestNet.bb
 hgLoadMafSummary -minSeqSize=1 -test $tDb $tDb.$qDb.rbestNet.summary \\
         $tDb.$qDb.rbestNet.maf.gz
 cut -f2- $tDb.$qDb.rbestNet.summary.tab | sort -k1,1 -k2,2n \\
         > $tDb.$qDb.rbestNet.summary.bed
 bedToBigBed -type=bed3+4 -as=mafSummary.as -tab \\
         $tDb.$qDb.rbestNet.summary.bed \\
         $targetSizes $tDb.$qDb.rbestNet.summary.bb
 rm -f $tDb.$qDb.rbestNet.txt $tDb.$qDb.rbestNet.summary.tab \\
         $tDb.$qDb.rbestNet.summary.bed
 _EOF_
       );
@@ -417,32 +417,32 @@
 | hgLoadNet -verbose=0 $tDb netRBest$QDb stdin
 _EOF_
       );
      }
 
     $bossScript->add(<<_EOF_
 cd $buildDir
 featureBits $tDb $QDbLink >&fb.$tDb.chainRBest.$QDb.txt
 cat fb.$tDb.chainRBest.$QDb.txt
 _EOF_
       );
   } else {
       $bossScript->add(<<_EOF_
 cd $runDir
 hgLoadChain -test -noBin -tIndex $tDb chainRBest$QDb $tDb.$qDb.rbest.chain.gz
-wget --no-check-certificate -O bigChain.as 'http://genome-source.soe.ucsc.edu/gitlist/kent.git/raw/master/src/hg/lib/bigChain.as'
-wget --no-check-certificate -O bigLink.as 'http://genome-source.soe.ucsc.edu/gitlist/kent.git/raw/master/src/hg/lib/bigLink.as'
+wget --no-check-certificate -O bigChain.as 'https://raw.githubusercontent.com/ucscGenomeBrowser/kent/refs/heads/master/src/hg/lib/bigChain.as'
+wget --no-check-certificate -O bigLink.as 'https://raw.githubusercontent.com/ucscGenomeBrowser/kent/refs/heads/master/src/hg/lib/bigLink.as'
 sed 's/.000000//' chain.tab | awk 'BEGIN {OFS="\\t"} {print \$2, \$4, \$5, \$11, 1000, \$8, \$3, \$6, \$7, \$9, \$10, \$1}' > chainRBest${QDb}.tab
 bedToBigBed -type=bed6+6 -as=bigChain.as -tab chainRBest${QDb}.tab $targetSizes chainRBest${QDb}.bb
 awk 'BEGIN {OFS="\\t"} {print \$1, \$2, \$3, \$5, \$4}' link.tab | sort -k1,1 -k2,2n > $QDbLink.tab
 bedToBigBed -type=bed4+1 -as=bigLink.as -tab $QDbLink.tab $targetSizes $QDbLink.bb
 set totalBases = `ave -col=2 $targetSizes | grep "^total" | awk '{printf "%d", \$2}'`
 set basesCovered = `bedSingleCover.pl $QDbLink.tab | ave -col=4 stdin | grep "^total" | awk '{printf "%d", \$2}'`
 set percentCovered = `echo \$basesCovered \$totalBases | awk '{printf "%.3f", 100.0*\$1/\$2}'`
 printf "%d bases of %d (%s%%) in intersection\\n" "\$basesCovered" "\$totalBases" "\$percentCovered" > ../fb.$tDb.chainRBest.$QDb.txt
 rm -f link.tab
 rm -f chain.tab
 if ( -s "$buildDir/axtChain/chainRBest${QDb}.bb" ) then
   mkdir -p /gbdb/$tDb/chainNet
   rm -f "/gbdb/$tDb/chainNet/$tDb.chainRBest$QDb.bb" "/gbdb/$tDb/chainNet/$tDb.chainRBest${QDb}Link.bb"
   ln -s "$buildDir/axtChain/chainRBest${QDb}.bb" "/gbdb/$tDb/chainNet/$tDb.chainRBest$QDb.bb"
    ln -s "$buildDir/axtChain/chainRBest${QDb}Link.bb" "/gbdb/$tDb/chainNet/$tDb.chainRBest${QDb}Link.bb"