4f6ea1808067647f43b31a4ed3e55723129de2f9
hiram
  Fri Sep 20 19:05:36 2024 -0700
genome-source has now become githubusercontent refs #34449

diff --git src/hg/utils/automation/doBlastzChainNet.pl src/hg/utils/automation/doBlastzChainNet.pl
index d7ee13b..4ad6ae7 100755
--- src/hg/utils/automation/doBlastzChainNet.pl
+++ src/hg/utils/automation/doBlastzChainNet.pl
@@ -985,32 +985,32 @@
 "It generates nets (without repeat/gap stats -- those are added later on
 $dbHost) from chains, and generates axt, maf and .over.chain from the nets.";
   my $bossScript = new HgRemoteScript("$runDir/netChains.csh", $workhorse,
 				      $runDir, $whatItDoes, $DEF);
   $bossScript->add(<<_EOF_
 # Make nets ("noClass", i.e. without rmsk/class stats which are added later):
 chainPreNet $inclHap $chain $defVars{SEQ1_LEN} $defVars{SEQ2_LEN} stdout \\
 | chainNet $inclHap stdin -minSpace=1 $defVars{SEQ1_LEN} $defVars{SEQ2_LEN} stdout /dev/null \\
 | netSyntenic stdin noClass.net
 
 # Make liftOver chains:
 netChainSubset -verbose=0 noClass.net $chain stdout \\
 | chainStitchId stdin stdout | gzip -c > $tDb.$qDb.over.chain.gz
 
 hgLoadChain -test -noBin -tIndex $tDb chainLiftOver$QDb $tDb.$qDb.over.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}' > chainLiftOver${QDb}.tab
 bedToBigBed -type=bed6+6 -as=bigChain.as -tab chainLiftOver${QDb}.tab $defVars{SEQ1_LEN} chainLiftOver${QDb}.bb
 awk 'BEGIN {OFS="\\t"} {print \$1, \$2, \$3, \$5, \$4}' link.tab | sort -k1,1 -k2,2n > chainLiftOver${QDb}Link.tab
 bedToBigBed -type=bed4+1 -as=bigLink.as -tab chainLiftOver${QDb}Link.tab $defVars{SEQ1_LEN} chainLiftOver${QDb}Link.bb
 set totalBases = `ave -col=2 $defVars{SEQ1_LEN} | grep "^total" | awk '{printf "%d", \$2}'`
 set basesCovered = `bedSingleCover.pl chainLiftOver${QDb}Link.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.$tDb.chainLiftOver${QDb}Link.txt
 rm -f link.tab chain.tab bigChain.as bigLink.as chainLiftOver${QDb}Link.tab chainLiftOver${QDb}.tab
 
 _EOF_
     );
   my $seq1Dir = $defVars{'SEQ1_DIR'};
   my $seq2Dir = $defVars{'SEQ2_DIR'};
   if ($splitRef) {
@@ -1062,32 +1062,32 @@
   stdout \\
 | gzip -c > ../mafNet/$tDb.$qDb.net.maf.gz
 _EOF_
       );
     if ($opt_trackHub) {
       $bossScript->add(<<_EOF_
 mkdir -p ../bigMaf
 ln -s ../mafNet/$tDb.$qDb.net.maf.gz ../bigMaf
 _EOF_
       );
     }
   }
   if ($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.net.maf.gz stdout \\
   | sort -k1,1 -k2,2n > $tDb.$qDb.net.txt
 bedToBigBed -itemsPerSlot=4 -type=bed3+1 -as=bigMaf.as -tab \\
   $tDb.$qDb.net.txt  $defVars{SEQ1_LEN} $tDb.$qDb.net.bb
 hgLoadMafSummary -minSeqSize=1 -test $tDb $tDb.$qDb.net.summary \\
   $tDb.$qDb.net.maf.gz
 cut -f2- $tDb.$qDb.net.summary.tab | sort -k1,1 -k2,2n \\
   > $tDb.$qDb.net.summary.bed
 bedToBigBed -type=bed3+4 -as=mafSummary.as -tab \\
         $tDb.$qDb.net.summary.bed $defVars{SEQ1_LEN} \\
         $tDb.$qDb.net.summary.bb
 rm -f $tDb.$qDb.net.txt $tDb.$qDb.net.summary.tab \\
         $tDb.$qDb.net.summary.bed
 _EOF_
       );
@@ -1144,32 +1144,32 @@
     hgLoadChain $tDb \${c}_chain$QDb \$f
 end
 _EOF_
       );
   } else {
     if (! $opt_trackHub && $dbExists && $tChromInfoExists ) {
       $bossScript->add(<<_EOF_
 cd $runDir
 hgLoadChain -tIndex $tDb chain$QDb $tDb.$qDb.all.chain.gz
 _EOF_
       );
     } else {
       $bossScript->add(<<_EOF_
 cd $runDir
 hgLoadChain -test -noBin -tIndex $tDb chain$QDb $tDb.$qDb.all.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}' > chain${QDb}.tab
 bedToBigBed -type=bed6+6 -as=bigChain.as -tab chain${QDb}.tab $defVars{SEQ1_LEN} chain${QDb}.bb
 awk 'BEGIN {OFS="\\t"} {print \$1, \$2, \$3, \$5, \$4}' link.tab | sort -k1,1 -k2,2n > chain${QDb}Link.tab
 bedToBigBed -type=bed4+1 -as=bigLink.as -tab chain${QDb}Link.tab $defVars{SEQ1_LEN} chain${QDb}Link.bb
 set totalBases = `ave -col=2 $defVars{SEQ1_LEN} | grep "^total" | awk '{printf "%d", \$2}'`
 set basesCovered = `bedSingleCover.pl chain${QDb}Link.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.$tDb.chain${QDb}Link.txt
 rm -f link.tab
 rm -f chain.tab
 _EOF_
       );
     }
   }
   if (! $isSelf) {
@@ -1824,32 +1824,32 @@
 _EOF_
       );
       if ($qDbExists && $qChromInfoExists) {
         $bossScript->add(<<_EOF_
   netFilter -minGap=10 $tDb.$qDb.syn.net.gz \\
     | hgLoadNet -verbose=0 $tDb netSyn$QDb stdin
 endif
 _EOF_
         );
       }
     } else {
       $bossScript->add(<<_EOF_
 set lineCount = `zcat $tDb.$qDb.syn.chain.gz | wc -l`
 if (\$lineCount > 0) then
   hgLoadChain -test -noBin -tIndex $tDb chainSyn$QDb $tDb.$qDb.syn.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}' > chainSyn${QDb}.tab
   bedToBigBed -type=bed6+6 -as=bigChain.as -tab chainSyn${QDb}.tab $defVars{SEQ1_LEN} chainSyn${QDb}.bb
   awk 'BEGIN {OFS="\\t"} {print \$1, \$2, \$3, \$5, \$4}' link.tab | sort -k1,1 -k2,2n > chainSyn${QDb}Link.tab
   bedToBigBed -type=bed4+1 -as=bigLink.as -tab chainSyn${QDb}Link.tab $defVars{SEQ1_LEN} chainSyn${QDb}Link.bb
   set totalBases = `ave -col=2 $defVars{SEQ1_LEN} | grep "^total" | awk '{printf "%d", \$2}'`
   set basesCovered = `bedSingleCover.pl chainSyn${QDb}Link.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.$tDb.chainSyn${QDb}Link.txt
 netFilter -minGap=10 $tDb.$qDb.syn.net.gz \\
   | hgLoadNet -test -noBin -warn -verbose=0 $tDb netSyn$QDb stdin
 mv align.tab netSyn$QDb.tab
   if ( -s "$buildDir/axtChain/chainSyn${QDb}.bb" ) then
     if ( "$tDb" !~ "GC*" ) then
       mkdir -p /gbdb/$tDb/chainNet
       rm -f "/gbdb/$tDb/chainNet/$tDb.chainSyn$QDb.bb" "/gbdb/$tDb/chainNet/$tDb.chainSyn${QDb}Link.bb"
@@ -1870,32 +1870,32 @@
     $defVars{'SEQ1_DIR'} $defVars{'SEQ2_DIR'} stdout \\
     | axtSort stdin stdout \\
     | axtToMaf -tPrefix=$tDb. -qPrefix=$qDb. stdin \\
       $defVars{SEQ1_LEN} $defVars{SEQ2_LEN} \\
       stdout \\
   | gzip -c > $tDb.$qDb.synNet.maf.gz
   md5sum $tDb.$qDb.syn.net.gz $tDb.$qDb.synNet.maf.gz > synNet.md5sum.txt
 endif
 _EOF_
       );
     if ($opt_trackHub) {
       $bossScript->add(<<_EOF_
 if (\$lineCount > 0) then
   mkdir -p ../bigMaf
   cd ../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 $tDb ../axtChain/$tDb.$qDb.synNet.maf.gz stdout \\
     | sort -k1,1 -k2,2n > $tDb.$qDb.synNet.txt
   bedToBigBed -itemsPerSlot=4 -type=bed3+1 -as=bigMaf.as -tab  $tDb.$qDb.synNet.txt \\
     $defVars{SEQ1_LEN} $tDb.$qDb.synNet.bb
   hgLoadMafSummary -minSeqSize=1 -test $tDb $tDb.$qDb.synNet.summary \\
         ../axtChain/$tDb.$qDb.synNet.maf.gz
   cut -f2- $tDb.$qDb.synNet.summary.tab | sort -k1,1 -k2,2n \\
         > $tDb.$qDb.synNet.summary.bed
   bedToBigBed -type=bed3+4 -as=mafSummary.as -tab \\
         $tDb.$qDb.synNet.summary.bed \\
         $defVars{SEQ1_LEN} $tDb.$qDb.synNet.summary.bb
   rm -f $tDb.$qDb.synNet.txt $tDb.$qDb.synNet.summary.tab \\
         $tDb.$qDb.synNet.summary.bed
   if ( -s "$buildDir/bigMaf/$tDb.$qDb.synNet.bb" ) then
     if ( "$tDb" !~ "GC*" ) then