80cbd6bce96d71ce3e03be94934cbff7b4521a4b hiram Thu May 7 13:14:24 2026 -0700 the trackDb update process for UCSC database assemblies refs #31811 diff --git src/hg/utils/otto/userRequests/chainNetTrackDb.pl src/hg/utils/otto/userRequests/chainNetTrackDb.pl new file mode 100755 index 00000000000..0930bf728a3 --- /dev/null +++ src/hg/utils/otto/userRequests/chainNetTrackDb.pl @@ -0,0 +1,521 @@ +#!/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 $tRow = `hgsql -N -e 'SELECT organism,scientificName,taxId,description FROM dbDb WHERE name="$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 $gRow = `hgsql -N -e 'SELECT commonName,scientificName,taxId,asmName FROM genark WHERE gcAccession="$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 $qRow = `hgsql -N -e 'SELECT organism,scientificName,taxId,description FROM dbDb WHERE name="$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"; + +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; + +############################################################################## +# 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 $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|$)/) { + $alreadyIncluded = 1; + last; + } + } + close($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; +} + +############################################################################## +# 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,,; + +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"; + $gitChanged = 0; +} + +if ($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; +} + +############################################################################## +# 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; + } +} + +exit 0;