95ee44a5d737970678a6d856d1228b908941de2c
hiram
  Fri Sep 20 19:00:51 2024 -0700
genome-source has now become githubusercontent refs #34449

diff --git src/hg/utils/automation/doNcbiRefSeq.pl src/hg/utils/automation/doNcbiRefSeq.pl
index 31516a6..ab28dea 100755
--- src/hg/utils/automation/doNcbiRefSeq.pl
+++ src/hg/utils/automation/doNcbiRefSeq.pl
@@ -604,32 +604,32 @@
 
   $bossScript->add(<<_EOF_
 # establish all variables to use here
 
 export db="$db"
 export asmId="$asmId"
 export verString="$verString"
 
 _EOF_
   );
   if (! $dbExists) {
     $bossScript->add(<<_EOF_
 export target2bit=$dbTwoBit
 
 twoBitInfo \$target2bit stdout | sort -k2,2nr > \$db.chrom.sizes
-wget -O bigGenePred.as 'http://genome-source.soe.ucsc.edu/gitlist/kent.git/raw/master/src/hg/lib/bigGenePred.as'
-wget -O bigPsl.as 'http://genome-source.soe.ucsc.edu/gitlist/kent.git/raw/master/src/hg/lib/bigPsl.as'
+wget -O bigGenePred.as 'https://raw.githubusercontent.com/ucscGenomeBrowser/kent/refs/heads/master/src/hg/lib/bigGenePred.as'
+wget -O bigPsl.as 'https://raw.githubusercontent.com/ucscGenomeBrowser/kent/refs/heads/master/src/hg/lib/bigPsl.as'
 
 ### overall gene track with both predicted and curated
 genePredToBigGenePred process/\$db.ncbiRefSeq.gp stdout | sort -k1,1 -k2,2n > \$db.ncbiRefSeq.bigGp
 genePredToBed -tab -fillSpace process/\$db.ncbiRefSeq.gp stdout \\
     | bedToExons stdin stdout | bedSingleCover.pl stdin > \$asmId.exons.bed
 export baseCount=`awk '{sum+=\$3-\$2}END{printf "%d", sum}' \$asmId.exons.bed`
 export asmSizeNoGaps=`grep sequences ../../\$asmId.faSize.txt | awk '{print \$5}'`
 export perCent=`echo \$baseCount \$asmSizeNoGaps | awk '{printf "%.3f", 100.0*\$1/\$2}'`
 bedToBigBed -type=bed12+8 -tab -as=bigGenePred.as -extraIndex=name \\
   \$db.ncbiRefSeq.bigGp \$db.chrom.sizes \\
     \$db.ncbiRefSeq.bb
 bigBedInfo \$db.ncbiRefSeq.bb | egrep "^itemCount:|^basesCovered:" \\
     | sed -e 's/,//g' > \$db.ncbiRefSeq.stats.txt
 LC_NUMERIC=en_US /usr/bin/printf "# ncbiRefSeq %s %'d %s %'d\\n" `cat \$db.ncbiRefSeq.stats.txt` | xargs echo
 ~/kent/src/hg/utils/automation/gpToIx.pl process/\$db.ncbiRefSeq.gp \\
@@ -776,31 +776,31 @@
     | grep -Fwf \$db.noRna.available.list \\
       | egrep "$nonNucNames" > missingChrMFa.psl
   if [ -s missingChrMFa.psl ]; then
     pslToBed missingChrMFa.psl stdout \\
       | twoBitToFa -bed=stdin \$target2bit stdout >> \$db.rna.fa
   fi
 fi
 
 if [ -s process/\$asmId.rna.cds ]; then
   cat process/\$asmId.rna.cds | grep '[0-9]\\+\\.\\.[0-9]\\+' \\
     | pslMismatchGapToBed -cdsFile=stdin -db=\$db -ignoreQNamePrefix=X \\
       process/\$asmId.\$db.psl.gz \$target2bit \\
         \$db.rna.fa ncbiRefSeqGenomicDiff || true
 
   if [ -s ncbiRefSeqGenomicDiff.bed ]; then
-    wget -O txAliDiff.as 'http://genome-source.soe.ucsc.edu/gitlist/kent.git/raw/master/src/hg/lib/txAliDiff.as'
+    wget -O txAliDiff.as 'https://raw.githubusercontent.com/ucscGenomeBrowser/kent/refs/heads/master/src/hg/lib/txAliDiff.as"
     bedToBigBed -type=bed9+ -tab -as=txAliDiff.as \\
       ncbiRefSeqGenomicDiff.bed \$db.chrom.sizes ncbiRefSeqGenomicDiff.bb
   else
     rm -f ncbiRefSeqGenomicDiff.bed
   fi
 fi
 
 export totalBases=`ave -col=2 \$db.chrom.sizes | grep "^total" | awk '{printf "%d", \$2}'`
 export basesCovered=`bedSingleCover.pl \$db.ncbiRefSeq.bigGp | ave -col=4 stdin | grep "^total" | awk '{printf "%d", \$2}'`
 export percentCovered=`echo \$basesCovered \$totalBases | awk '{printf "%.3f", 100.0*\$1/\$2}'`
 printf "%d bases of %d (%s%%) in intersection\\n" "\$basesCovered" \\
    "\$totalBases" "\$percentCovered" > fb.ncbiRefSeq.\$db.txt
 printf "%d bases of %d (%s%%) in intersection\\n" "\$baseCount" "\$asmSizeNoGaps" "\$perCent" > fb.\$asmId.ncbiRefSeq.txt
 
 rm -f \$db.ncbiRefSeq.bigGp \$asmId.exons.bed