3eaf4d4b81181d543facc006791bbfc433f26528 hiram Mon Jun 1 09:26:37 2020 -0700 no need to fail on certificate from genome-source.soe.ucsc.edu refs #25625 diff --git src/hg/utils/automation/doRecipBest.pl src/hg/utils/automation/doRecipBest.pl index 79652e4..b575d7a 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 -O bigMaf.as 'http://genome-source.soe.ucsc.edu/gitlist/kent.git/raw/master/src/hg/lib/bigMaf.as' -wget -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 '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' mafToBigMaf $tDb $tDb.$qDb.rbestNet.maf.gz stdout \\ | sort -k1,1 -k2,2n > $tDb.$qDb.rbestNet.txt bedToBigBed -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_ ); @@ -412,32 +412,32 @@ | 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 -O bigChain.as 'http://genome-source.soe.ucsc.edu/gitlist/kent.git/raw/master/src/hg/lib/bigChain.as' -wget -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 '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' 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 _EOF_ ); } # else if (! $opt_trackHub && $dbExists) $bossScript->execute();