93026392de53b8abf15a3605b88aa6d7fb0f962d hiram Mon May 11 12:05:53 2026 -0700 do not need to run "make" in the trackDb since the "include" line is now a comment refs #31811 diff --git src/hg/utils/otto/userRequests/chainNetTrackDb.pl src/hg/utils/otto/userRequests/chainNetTrackDb.pl index fd7c05f260f..89c74cfe32c 100755 --- src/hg/utils/otto/userRequests/chainNetTrackDb.pl +++ src/hg/utils/otto/userRequests/chainNetTrackDb.pl @@ -1,521 +1,535 @@ #!/usr/bin/env perl # chainNetTrackDb.pl - generate a chainNet trackDb stanza for a UCSC native # target database, by probing axtChain/*.bb files in the current build # directory. Writes the result to the kent trackDb tree at # ~/kent/src/hg/makeDb/trackDb/<clade>/<targetDb>/<targetDb>.<queryAcc>.chainNet.ra # # Run from a build directory, e.g.: # /hive/data/genomes/ce11/bed/blastz.GCA_000180635.4.swap # /hive/data/genomes/hg38/bed/lastzMm39.YYYY-MM-DD # # usage: chainNetTrackDb.pl <targetDb> <queryDb> # # Probes (ignoring any *quick* files): # ./axtChain/chain<Query>.bb + chain<Query>Link.bb # ./axtChain/chainLiftOver<Query>.bb + chainLiftOver<Query>Link.bb # ./axtChain/chainSyn<Query>.bb + chainSyn<Query>Link.bb # ./axtChain/chainRBest<Query>.bb + chainRBest<Query>Link.bb # ./axtChain/<qAcc>.net.bb + <qAcc>.net.summary.bb # ./axtChain/<qAcc>.synNet.bb + <qAcc>.synNet.summary.bb # ./axtChain/<qAcc>.rbestNet.bb + <qAcc>.rbestNet.summary.bb # Where: # qAcc = queryDb stripped to GC[AF]_NNNNNNNNN.N for GenArk, else queryDb # Query = ucfirst(qAcc) # # Metadata sources: # target (UCSC native): hgcentraltest.dbDb # query GenArk: hgcentraltest.genark + assembly_report.txt # query UCSC native: hgcentraltest.dbDb use strict; use warnings; use Cwd qw(getcwd abs_path); use File::Path qw(make_path); use Fcntl qw(:flock); my @months = qw( zero Jan. Feb. Mar. Apr. May Jun. Jul. Aug. Sep. Oct. Nov. Dec. ); sub usage { printf STDERR "usage: chainNetTrackDb.pl <targetDb> <queryDb>\n"; printf STDERR " Run from a build directory containing an axtChain/ subdir.\n"; printf STDERR " Probes axtChain/*.bb (ignoring *quick*) to determine which\n"; printf STDERR " chainNet stanzas to emit, and writes them to:\n"; printf STDERR " ~/kent/src/hg/makeDb/trackDb/<clade>/<targetDb>/<targetDb>.<qAcc>.chainNet.ra\n"; printf STDERR " Only handles UCSC native targetDb; GenArk targets use doTrackDb.bash.\n"; exit 255; } usage() if (scalar(@ARGV) != 2); my $targetDb = shift; my $queryDb = shift; if ($targetDb =~ /^GC[AF]_/) { printf STDERR "ERROR: GenArk target '%s' is not handled here; use doTrackDb.bash\n", $targetDb; exit 255; } my $axtChain = "axtChain"; if (! -d $axtChain) { printf STDERR "ERROR: must be run from a build directory; no %s/ in cwd %s\n", $axtChain, getcwd(); exit 255; } # normalize query - strip _asmName suffix for GenArk my $qAcc = $queryDb; if ($queryDb =~ /^(GC[AF]_\d+\.\d+)/) { $qAcc = $1; } my $Query = ucfirst($qAcc); ############################################################################## # look up target metadata from dbDb ############################################################################## my $tRow = `/cluster/bin/x86_64/hgsql -N -e 'SELECT organism,scientificName,taxId,description FROM dbDb WHERE name="$targetDb"' hgcentraltest 2>/dev/null`; chomp $tRow; if (length($tRow) < 1) { printf STDERR "ERROR: target db '%s' not found in hgcentraltest.dbDb\n", $targetDb; exit 255; } my ($tOrganism, $tSciName, $tTaxId, $tDesc) = split(/\t/, $tRow); $tOrganism = "" if (!defined $tOrganism); ############################################################################## # look up query metadata ############################################################################## my $qOrganism = ""; my $qSciName = ""; my $qTaxId = ""; my $qDate = ""; my $qAsmName = ""; if ($qAcc =~ /^GC[AF]_/) { # GenArk: get commonName/scientificName/taxId/asmName from the genark # table; only fall back to assembly_report.txt for the assembly date, # which the genark table does not carry. my $gRow = `/cluster/bin/x86_64/hgsql -N -e 'SELECT commonName,scientificName,taxId,asmName FROM genark WHERE gcAccession="$qAcc"' hgcentraltest 2>/dev/null`; chomp $gRow; if (length($gRow) < 1) { printf STDERR "ERROR: GenArk accession '%s' not found in hgcentraltest.genark\n", $qAcc; exit 255; } ($qOrganism, $qSciName, $qTaxId, $qAsmName) = split(/\t/, $gRow); $qOrganism = "" if (!defined $qOrganism); $qSciName = "" if (!defined $qSciName); $qTaxId = "" if (!defined $qTaxId); $qAsmName = "" if (!defined $qAsmName); # commonName may be empty; fall back to scientificName if (length($qOrganism) < 1) { $qOrganism = $qSciName; } # assembly_report.txt: only needed for the assembly date my $gcX = substr($qAcc, 0, 3); my $d0 = substr($qAcc, 4, 3); my $d1 = substr($qAcc, 7, 3); my $d2 = substr($qAcc, 10, 3); my $hubBuild = "/hive/data/genomes/asmHubs/allBuild/$gcX/$d0/$d1/$d2"; my $ncbiPath = "/hive/data/outside/ncbi/genomes/$gcX/$d0/$d1/$d2"; my $asmReport = `ls -d $hubBuild/${qAcc}*/download/*assembly_report.txt 2>/dev/null | head -1`; chomp $asmReport; if (! -s $asmReport) { $asmReport = `ls -d $ncbiPath/${qAcc}*/${qAcc}*assembly_report.txt 2>/dev/null | head -1`; chomp $asmReport; } if (-s $asmReport) { my $ymd = `grep -i 'date:' $asmReport | head -1 | tr -d '\r' | sed -e 's/.*date: *//i;'`; chomp $ymd; if ($ymd =~ /^(\d{4})-(\d{1,2})/) { my ($y, $m) = ($1, $2 + 0); $qDate = sprintf("%s %d", $months[$m], $y) if ($m >= 1 && $m <= 12); } } } else { # UCSC native: dbDb has organism, sciName, taxId, description my $qRow = `/cluster/bin/x86_64/hgsql -N -e 'SELECT organism,scientificName,taxId,description FROM dbDb WHERE name="$qAcc"' hgcentraltest 2>/dev/null`; chomp $qRow; if (length($qRow) < 1) { printf STDERR "ERROR: query db '%s' not found in hgcentraltest.dbDb\n", $qAcc; exit 255; } my $desc; ($qOrganism, $qSciName, $qTaxId, $desc) = split(/\t/, $qRow); $qOrganism = "" if (!defined $qOrganism); # dbDb.description is typically the assembly date string, e.g. "Apr. 2017" $qDate = defined($desc) ? $desc : ""; } ############################################################################## # probe axtChain/ for available files ############################################################################## my $hasChain = (-s "$axtChain/chain${Query}.bb" && -s "$axtChain/chain${Query}Link.bb"); my $hasLO = (-s "$axtChain/chainLiftOver${Query}.bb" && -s "$axtChain/chainLiftOver${Query}Link.bb"); my $hasSyn = (-s "$axtChain/chainSyn${Query}.bb" && -s "$axtChain/chainSyn${Query}Link.bb"); my $hasRBest = (-s "$axtChain/chainRBest${Query}.bb" && -s "$axtChain/chainRBest${Query}Link.bb"); my $hasNet = (-s "$axtChain/${qAcc}.net.bb" && -s "$axtChain/${qAcc}.net.summary.bb"); my $hasSynNet = (-s "$axtChain/${qAcc}.synNet.bb" && -s "$axtChain/${qAcc}.synNet.summary.bb"); my $hasRBestNet = (-s "$axtChain/${qAcc}.rbestNet.bb" && -s "$axtChain/${qAcc}.rbestNet.summary.bb"); if (!$hasChain && !$hasLO && !$hasSyn && !$hasRBest && !$hasNet && !$hasSynNet && !$hasRBestNet) { printf STDERR "ERROR: no chain/net .bb files found in %s/ for %s\n", $axtChain, $Query; exit 255; } ############################################################################## # resolve output dir in the dedicated otto kent clone, take an exclusive # lock on it to serialize concurrent invocations, and verify the working # tree is pristine before we modify anything. ############################################################################## my $kentTree = $ENV{OTTO_KENT_TREE} // "/hive/data/outside/genark/ottoKent/kent"; if (! -d "$kentTree/.git") { printf STDERR "ERROR: not a git working tree: %s\n", $kentTree; exit 255; } # blocking exclusive lock on a dotfile inside .git so it stays out of the # tracked tree. Kernel releases the lock on process exit, so no cleanup # is needed. $lockFh stays in scope until script end. my $lockPath = "$kentTree/.git/chainNetTrackDb.lock"; open(my $lockFh, '>>', $lockPath) or die "ERROR: cannot open lock '$lockPath': $!\n"; if (!flock($lockFh, LOCK_EX)) { die "ERROR: cannot acquire lock '$lockPath': $!\n"; } # refuse to run on a dirty tree -- this clone exists only for this script, # so any uncommitted state means something went wrong last time. my $dirty = `git -C "$kentTree" status --porcelain 2>&1`; if (length($dirty) > 0) { printf STDERR "ERROR: '%s' has uncommitted changes:\n%s", $kentTree, $dirty; exit 255; } my @hits = grep { -d $_ } glob("$kentTree/src/hg/makeDb/trackDb/*/$targetDb"); if (scalar(@hits) != 1) { printf STDERR "ERROR: expected exactly 1 trackDb dir for '%s', found %d:\n", $targetDb, scalar(@hits); printf STDERR " %s\n", $_ for @hits; exit 255; } my $outDir = $hits[0]; my $outFile = "$outDir/$targetDb.$qAcc.chainNet.ra"; ############################################################################## # create /gbdb/<targetDb>/chainNet/ and symlink the axtChain/*.bb files there # so the bigDataUrl/linkDataUrl/summary paths emitted below resolve. # Each link in /gbdb/<tDb>/chainNet/ has the prefix '<tDb>.' to match the # '$D.' prefix used in the trackDb stanzas. ############################################################################## my $axtAbs = abs_path($axtChain); if (!defined($axtAbs) || ! -d $axtAbs) { printf STDERR "ERROR: cannot resolve absolute path for %s/\n", $axtChain; exit 255; } my $gbdbDir = "/gbdb/$targetDb/chainNet"; if (! -d $gbdbDir) { make_path($gbdbDir); if (! -d $gbdbDir) { printf STDERR "ERROR: cannot create %s: %s\n", $gbdbDir, $!; exit 255; } } # pairs of (file in axtChain/, link basename in /gbdb/<tDb>/chainNet/) # the link basename gets the '<targetDb>.' prefix so it matches '$D.<...>' my @linkPairs = (); if ($hasChain) { push @linkPairs, ["chain${Query}.bb", "$targetDb.chain${Query}.bb"]; push @linkPairs, ["chain${Query}Link.bb", "$targetDb.chain${Query}Link.bb"]; } if ($hasLO) { push @linkPairs, ["chainLiftOver${Query}.bb", "$targetDb.chainLiftOver${Query}.bb"]; push @linkPairs, ["chainLiftOver${Query}Link.bb", "$targetDb.chainLiftOver${Query}Link.bb"]; } if ($hasSyn) { push @linkPairs, ["chainSyn${Query}.bb", "$targetDb.chainSyn${Query}.bb"]; push @linkPairs, ["chainSyn${Query}Link.bb", "$targetDb.chainSyn${Query}Link.bb"]; } if ($hasRBest) { push @linkPairs, ["chainRBest${Query}.bb", "$targetDb.chainRBest${Query}.bb"]; push @linkPairs, ["chainRBest${Query}Link.bb", "$targetDb.chainRBest${Query}Link.bb"]; } if ($hasNet) { push @linkPairs, ["${qAcc}.net.bb", "$targetDb.${qAcc}.net.bb"]; push @linkPairs, ["${qAcc}.net.summary.bb", "$targetDb.${qAcc}.net.summary.bb"]; } if ($hasSynNet) { push @linkPairs, ["${qAcc}.synNet.bb", "$targetDb.${qAcc}.synNet.bb"]; push @linkPairs, ["${qAcc}.synNet.summary.bb", "$targetDb.${qAcc}.synNet.summary.bb"]; } if ($hasRBestNet) { push @linkPairs, ["${qAcc}.rbestNet.bb", "$targetDb.${qAcc}.rbestNet.bb"]; push @linkPairs, ["${qAcc}.rbestNet.summary.bb", "$targetDb.${qAcc}.rbestNet.summary.bb"]; } for my $pair (@linkPairs) { my ($srcName, $dstName) = @$pair; my $src = "$axtAbs/$srcName"; my $dst = "$gbdbDir/$dstName"; if (-l $dst || -e $dst) { if (!unlink($dst)) { printf STDERR "ERROR: cannot remove existing '%s': %s\n", $dst, $!; exit 255; } } if (!symlink($src, $dst)) { printf STDERR "ERROR: symlink '%s' -> '%s' failed: %s\n", $dst, $src, $!; exit 255; } } ############################################################################## # compose stanza, write to file ############################################################################## my $shortOrg = (length($qOrganism) > 0) ? $qOrganism : $qAcc; my $longTail; if ($qAsmName ne "") { $longTail = "${qAcc}_${qAsmName}"; } else { $longTail = $qAcc; } my $longInner = (length($qDate) > 0) ? "$qDate $longTail" : $longTail; -printf STDERR "### writing to $outFile\n"; +# printf STDERR "### writing to $outFile\n"; open(my $fh, '>', $outFile) or die "ERROR: cannot write '$outFile': $!\n"; printf $fh "##############################################################################\n"; printf $fh "# %s - %s - %s - taxId: %s\n", $qAcc, $shortOrg, $qSciName, $qTaxId; printf $fh "##############################################################################\n"; printf $fh "track chainNet%s\n", $Query; printf $fh "compositeTrack on\n"; printf $fh "shortLabel %s Chain/Net\n", $shortOrg; printf $fh "longLabel %s (%s), Chain and Net Alignments\n", $shortOrg, $longInner; printf $fh "subGroup1 view Views chain=Chain net=Net\n"; printf $fh "dragAndDrop subTracks\n"; printf $fh "visibility hide\n"; printf $fh "group compGeno\n"; printf $fh "noInherit on\n"; printf $fh "priority 100.1\n"; printf $fh "color 0,0,0\n"; printf $fh "altColor 100,50,0\n"; printf $fh "type bed 3\n"; printf $fh "sortOrder view=+\n"; printf $fh "matrix 16 91,-114,-31,-123,-114,100,-125,-31,-31,-125,100,-114,-123,-31,-114,91\n"; printf $fh "chainMinScore 3000\n"; printf $fh "chainLinearGap medium\n"; printf $fh "matrixHeader A, C, G, T\n"; printf $fh "otherDb %s\n", $qAcc; printf $fh "html chainNet\n"; printf $fh "\n"; ############################################################################## # Chain view ############################################################################## if ($hasChain || $hasLO || $hasSyn || $hasRBest) { printf $fh " track chainNet%sViewchain\n", $Query; printf $fh " shortLabel Chain\n"; printf $fh " view chain\n"; printf $fh " visibility pack\n"; printf $fh " parent chainNet%s\n", $Query; printf $fh " spectrum on\n"; printf $fh "\n"; if ($hasChain) { printf $fh " track chain%s\n", $Query; printf $fh " parent chainNet%sViewchain\n", $Query; printf $fh " subGroups view=chain\n"; printf $fh " shortLabel %s Chain\n", $shortOrg; printf $fh " longLabel %s (%s) Chained Alignments\n", $shortOrg, $longInner; printf $fh " type bigChain %s\n", $qAcc; printf $fh " bigDataUrl /gbdb/\$D/chainNet/\$D.chain%s.bb\n", $Query; printf $fh " linkDataUrl /gbdb/\$D/chainNet/\$D.chain%sLink.bb\n", $Query; printf $fh "\n"; } if ($hasLO) { printf $fh " track chainLiftOver%s\n", $Query; printf $fh " parent chainNet%sViewchain\n", $Query; printf $fh " subGroups view=chain\n"; printf $fh " shortLabel %s liftOverChain\n", $shortOrg; printf $fh " longLabel %s (%s) Lift Over Chained Alignments\n", $shortOrg, $longInner; printf $fh " type bigChain %s\n", $qAcc; printf $fh " bigDataUrl /gbdb/\$D/chainNet/\$D.chainLiftOver%s.bb\n", $Query; printf $fh " linkDataUrl /gbdb/\$D/chainNet/\$D.chainLiftOver%sLink.bb\n", $Query; printf $fh "\n"; } if ($hasSyn) { printf $fh " track chainSyn%s\n", $Query; printf $fh " parent chainNet%sViewchain\n", $Query; printf $fh " subGroups view=chain\n"; printf $fh " shortLabel %s synChain\n", $shortOrg; printf $fh " longLabel %s (%s) Syntenic Chained Alignments\n", $shortOrg, $longInner; printf $fh " type bigChain %s\n", $qAcc; printf $fh " bigDataUrl /gbdb/\$D/chainNet/\$D.chainSyn%s.bb\n", $Query; printf $fh " linkDataUrl /gbdb/\$D/chainNet/\$D.chainSyn%sLink.bb\n", $Query; printf $fh "\n"; } if ($hasRBest) { printf $fh " track chainRBest%s\n", $Query; printf $fh " parent chainNet%sViewchain\n", $Query; printf $fh " subGroups view=chain\n"; printf $fh " shortLabel %s rBestChain\n", $shortOrg; printf $fh " longLabel %s (%s) Reciprocal Best Chained Alignments\n", $shortOrg, $longInner; printf $fh " type bigChain %s\n", $qAcc; printf $fh " bigDataUrl /gbdb/\$D/chainNet/\$D.chainRBest%s.bb\n", $Query; printf $fh " linkDataUrl /gbdb/\$D/chainNet/\$D.chainRBest%sLink.bb\n", $Query; printf $fh "\n"; } } ############################################################################## # Net view ############################################################################## if ($hasNet || $hasSynNet || $hasRBestNet) { printf $fh " track mafNet%sViewnet\n", $Query; printf $fh " shortLabel Net\n"; printf $fh " view net\n"; printf $fh " visibility full\n"; printf $fh " parent chainNet%s\n", $Query; printf $fh "\n"; if ($hasNet) { printf $fh " track net%s\n", $Query; printf $fh " parent mafNet%sViewnet\n", $Query; printf $fh " subGroups view=net\n"; printf $fh " shortLabel %s mafNet\n", $shortOrg; printf $fh " longLabel %s (%s) mafNet Alignment\n", $shortOrg, $longInner; printf $fh " type bigMaf\n"; printf $fh " bigDataUrl /gbdb/\$D/chainNet/\$D.%s.net.bb\n", $qAcc; printf $fh " summary /gbdb/\$D/chainNet/\$D.%s.net.summary.bb\n", $qAcc; printf $fh " speciesOrder %s\n", $qAcc; printf $fh " speciesLabels %s=\"%s\"\n", $qAcc, $shortOrg; printf $fh "\n"; } if ($hasSynNet) { printf $fh " track synNet%s\n", $Query; printf $fh " parent mafNet%sViewnet\n", $Query; printf $fh " subGroups view=net\n"; printf $fh " shortLabel %s synNet\n", $shortOrg; printf $fh " longLabel %s (%s) Syntenic Net Alignment\n", $shortOrg, $longInner; printf $fh " type bigMaf\n"; printf $fh " bigDataUrl /gbdb/\$D/chainNet/\$D.%s.synNet.bb\n", $qAcc; printf $fh " summary /gbdb/\$D/chainNet/\$D.%s.synNet.summary.bb\n", $qAcc; printf $fh " speciesOrder %s\n", $qAcc; printf $fh " speciesLabels %s=\"%s\"\n", $qAcc, $shortOrg; printf $fh "\n"; } if ($hasRBestNet) { printf $fh " track rbestNet%s\n", $Query; printf $fh " parent mafNet%sViewnet\n", $Query; printf $fh " subGroups view=net\n"; printf $fh " shortLabel %s rBestNet\n", $shortOrg; printf $fh " longLabel %s (%s) Reciprocal Best Net Alignment\n", $shortOrg, $longInner; printf $fh " type bigMaf\n"; printf $fh " bigDataUrl /gbdb/\$D/chainNet/\$D.%s.rbestNet.bb\n", $qAcc; printf $fh " summary /gbdb/\$D/chainNet/\$D.%s.rbestNet.summary.bb\n", $qAcc; printf $fh " speciesOrder %s\n", $qAcc; printf $fh " speciesLabels %s=\"%s\"\n", $qAcc, $shortOrg; printf $fh "\n"; } } close($fh); -printf STDERR "wrote %s\n", $outFile; +# printf STDERR "wrote %s\n", $outFile; ############################################################################## # ensure trackDb.ra in the same dir has an 'include <basename> alpha' line # for the newly written .ra file; append it if not already present ############################################################################## my $trackDbRa = "$outDir/trackDb.ra"; my $baseName = "$targetDb.$qAcc.chainNet.ra"; -my $includeLn = "include $baseName alpha"; +my $includeLn = "# include $baseName alpha"; my $alreadyIncluded = 0; if (-e $trackDbRa) { open(my $rh, '<', $trackDbRa) or die "ERROR: cannot read '$trackDbRa': $!\n"; while (my $line = <$rh>) { - if ($line =~ /^\s*include\s+\Q$baseName\E(\s|$)/) { + if ($line =~ /^#\s*include\s+\Q$baseName\E(\s|$)/) { $alreadyIncluded = 1; last; } } close($rh); } if (!$alreadyIncluded) { open(my $ah, '>>', $trackDbRa) or die "ERROR: cannot append to '$trackDbRa': $!\n"; printf $ah "%s\n", $includeLn; close($ah); - printf STDERR "appended '%s' to %s\n", $includeLn, $trackDbRa; +# printf STDERR "appended '%s' to %s\n", $includeLn, $trackDbRa; } ############################################################################## # stage the new .ra (and trackDb.ra if it changed) and commit. # Requires user.name / user.email configured in the clone's git config. ############################################################################## my $newRel = $outFile; $newRel =~ s,^\Q$kentTree/\E,,; my $tdbRel = $trackDbRa; $tdbRel =~ s,^\Q$kentTree/\E,,; +### update this source tree to catch up to the outside world +if (system('git', '-C', $kentTree, 'pull') != 0) { + printf STDERR "ERROR: 'git pull' failed in %s\n", $kentTree; + exit 255; +} + if (system('git', '-C', $kentTree, 'add', '--', $newRel, $tdbRel) != 0) { printf STDERR "ERROR: 'git add' failed in %s\n", $kentTree; exit 255; } my $gitChanged = 1; # nothing to commit if neither file actually changed (idempotent re-runs) if (system('git', '-C', $kentTree, 'diff', '--cached', '--quiet') == 0) { - printf STDERR "no changes to source tree\n"; +# printf STDERR "no changes to source tree\n"; $gitChanged = 0; } if ($gitChanged) { my $msg = sprintf("chainNet trackDb for %s %s, otto liftOver", $targetDb, $qAcc); if (system('git', '-C', $kentTree, 'commit', '-m', $msg) != 0) { printf STDERR "ERROR: 'git commit' failed in %s\n", $kentTree; exit 255; } - printf STDERR "committed: %s\n", $msg; +# printf STDERR "committed: %s\n", $msg; + + # push so the tree doesn't accumulate local commits that block future + # 'git pull' / fast-forward updates from master. + if (system('git', '-C', $kentTree, 'push') != 0) { + printf STDERR "ERROR: 'git push' failed in %s\n", $kentTree; + exit 255; + } +# printf STDERR "pushed to remote\n"; } ############################################################################## # build/install trackDb for the target database (default release + alpha) # so the new tracks show up in the genome browser. ############################################################################## -my $tdbDir = "$kentTree/src/hg/makeDb/trackDb"; -for my $args ( ["DBS=$targetDb"], ["DBS=$targetDb", "alpha"] ) { - printf STDERR "make -c %s %s\n", $tdbDir, $args->[0]; - if (system('make', '-C', $tdbDir, @$args) != 0) { - printf STDERR "ERROR: 'make -C %s %s' failed\n", - $tdbDir, join(' ', @$args); - exit 255; - } -} +# my $tdbDir = "$kentTree/src/hg/makeDb/trackDb"; +# for my $args ( ["DBS=$targetDb"], ["DBS=$targetDb", "alpha"] ) { +# # printf STDERR "make -c %s %s\n", $tdbDir, $args->[0]; +# if (system('make', '-C', $tdbDir, @$args) != 0) { +# printf STDERR "ERROR: 'make -C %s %s' failed\n", +# $tdbDir, join(' ', @$args); +# exit 255; +# } +# } exit 0;