1c41dff03108b4818777b9c9914e81c72555163f hiram Tue Sep 29 12:28:41 2026 -0700 miniMap2 now with swap option refs #34360 diff --git src/hg/utils/automation/doMiniMap2.pl src/hg/utils/automation/doMiniMap2.pl index 0ed60ca8612..8b14cec865f 100755 --- src/hg/utils/automation/doMiniMap2.pl +++ src/hg/utils/automation/doMiniMap2.pl @@ -1,939 +1,1083 @@ #!/usr/bin/env perl # DO NOT EDIT the /cluster/bin/scripts copy of this file -- # edit ~/kent/src/hg/utils/automation/doMiniMap2.pl instead. # doMiniMap2.pl -- same-species / same-haplotype liftOver pipeline, # modeled directly on doSameSpeciesLiftOver.pl, but using minimap2 # instead of blat as the alignment engine. # # Intended use: two very similar same-species assemblies where blat's # -fastMap query-chunking dance isn't needed and minimap2's splice-free # asm5/asm10/asm20 presets do a better job with the larger indels and # structural differences you see between the two haplotypes of a # diploid (trio-binned or hifiasm/verkko dual-assembly) genome, or # between two closely related strain assemblies. # # Requires the kent command pafToPsl (PAF+cigar -> PSL) so the existing # axtChain/chainNet/netChainSubset toolchain can be reused unchanged. use Getopt::Long; use warnings; use strict; use FindBin qw($Bin); use lib "$Bin"; use File::Basename qw(basename); use HgAutomate; use HgRemoteScript; use HgStepManager; use AssemblyDivergence qw(mashDistance choosePipeline $mashAsm5Max $mashAsm10Max $mashLastzMin $mashWarnMax); use AsmHub qw(accessionFromPath asmBuildDir asmIdToPath); # Option variable names, both common and peculiar to this script: use vars @HgAutomate::commonOptionVars; use vars @HgStepManager::optionVars; use vars qw/ $opt_buildDir $opt_target2Bit $opt_targetSizes $opt_query2Bit $opt_querySizes $opt_minimapPreset $opt_minimapCpu $opt_minimapSecondaryN $opt_minimapSecondaryRatio $opt_chainRam $opt_chainCpu $opt_regenerateMash + $opt_swap + $opt_swapDir /; # Specify the steps supported with -continue / -stop: my $stepper = new HgStepManager( [ { name => 'align', func => \&doAlign }, { name => 'chain', func => \&doChain }, { name => 'net', func => \&doNet }, { name => 'load', func => \&doLoad }, { name => 'cleanup', func => \&doCleanup }, ] ); # Option defaults: my $dbHost = 'hgwdev'; my $ramG = '24g'; # minimap2 index + 8 threads on a whole genome needs headroom # minimapPreset is normally left undef and picked automatically by # estimateDivergence() (mash distance -> asm5/asm10/asm20); -minimapPreset # overrides that and skips the mash run entirely. my $minimapPreset; my $minimapCpu = 8; # -t N threads given to each minimap2 job # Secondary alignments are kept (not '--secondary=no') so axtChain/chainNet # see the same kind of overlapping candidate alignments a lastz/blastz run # would give them, and can use genome-scale synteny context to arbitrate # ambiguous/duplicated regions -- rather than trusting minimap2's own local, # per-query-region primary/secondary call alone. Defaults match minimap2's # own -N/-p defaults; only override via -minimapSecondaryN/-Ratio if you # have a specific reason to. my $minimapSecondaryN = 5; # -N INT to minimap2 my $minimapSecondaryRatio = 0.8; # -p FLOAT to minimap2 my $chainRam = '16g'; # -chainRam=Ng argument my $chainCpu = 1; # -chainCpu=N argument # mash distance thresholds ($mashAsm5Max/$mashAsm10Max/$mashLastzMin/ # $mashWarnMax) used to pick a preset (or reject the pair outright) come # from AssemblyDivergence.pm, shared with mashDistance.pl and anything # else that needs to triage a pair between this pipeline and # doBlastzChainNet.pl. my $base = $0; $base =~ s/^(.*\/)?//; sub usage { # Usage / help / self-documentation: my ($status, $detailed) = @_; # Basic help (for incorrect usage): print STDERR " usage: $base fromDb toDb options: "; print STDERR $stepper->getOptionHelp(); print STDERR <<_EOF_ -buildDir dir Use dir instead of default $HgAutomate::clusterData/\$fromDb/$HgAutomate::trackBuild/miniMap2\$ToDb.\$date (necessary when continuing at a later date). -target2Bit /path/target.2bit Full path to target sequence (fromDb) -query2Bit /path/query.2bit Full path to query sequence (toDb) -targetSizes /path/target.chrom.sizes Full path to target chrom.sizes (fromDb) -querySizes /path/query.chrom.sizes Full path to query chrom.sizes (toDb) -minimapPreset asm5|asm10|asm20 minimap2 -x preset to use. By default this is chosen automatically via AssemblyDivergence.pm (same logic as the standalone mashDistance.pl): mash sketches \$fromDb and \$toDb and picks a preset from the mash distance between them (< $mashAsm5Max -> asm5, < $mashAsm10Max -> asm10, < $mashLastzMin -> asm20). At or above $mashLastzMin this script refuses to run -- that pair looks too diverged for minimap2's asm* presets; use doBlastzChainNet.pl instead, or give -minimapPreset to skip the mash run and force a specific preset anyway. -minimapCpu N Threads given to each minimap2 cluster job (-t N), default: $minimapCpu -ram Ng Cluster ram size for minimap2, default: -ram=$ramG -minimapSecondaryN N minimap2 -N: max secondary alignments retained per primary hit, default: $minimapSecondaryN. Secondary alignments are kept (not -secondary=no) so axtChain/chainNet get the same kind of overlapping candidate alignments a lastz run would give them, and can resolve ambiguous/duplicated regions using genome-scale synteny context instead of relying on minimap2's own local primary/secondary call alone. -minimapSecondaryRatio F minimap2 -p: minimum secondary-to-primary score ratio to keep a secondary at all, default: $minimapSecondaryRatio -chainRam Ng Cluster ram size for chain step, default: -chainRam=$chainRam -chainCpu N Cluster CPUs number for chain step, default: -chainCpu=$chainCpu -regenerateMash Force the mash divergence check to re-sketch and overwrite even if a cached .msh (GenArk mashSketch/ cache or \$buildDir/mashDistance.txt) already exists. Ignored if -minimapPreset is also given, since that skips the mash run entirely. + -swap fromDb toDb are the same as the already-completed + primary run's; instead of aligning again, chainSwap + the primary run's axtChain/all.chain.gz (requires it + to already exist) and build the toDb-to-fromDb + liftOver/quickLift chain from that, in + -swapDir (default: toDb's own build root)/miniMap2.\$fromDb.swap + -swapDir dir Use dir instead of the default -swap work directory. _EOF_ ; print STDERR &HgAutomate::getCommonOptionHelp('dbHost' => $dbHost, 'workhorse' => '', 'fileServer' => '', 'ram' => $ramG, 'minimapCpu' => $minimapCpu, 'bigClusterHub' => ''); print STDERR " Automates a same-species/same-haplotype liftOver (minimap2/chain/net) pipeline, patterned after doSameSpeciesLiftOver.pl but using minimap2 in place of blat -fastMap: align: Aligns the assemblies using minimap2 -cx \$minimapPreset on a big cluster, one job per target sequence against the full query genome, then converts PAF+cigar to PSL with pafToPsl. chain: Chains the alignments on a big cluster. net: Nets the alignments, uses netChainSubset to extract liftOver chains. load: Installs liftOver chain files, calls hgAddLiftOverChain on $dbHost. cleanup: Removes or compresses intermediate files. +With -swap (not a normal stepper step -- see -swap above), chainSwap the +primary run's all.chain.gz and reuse the net/load logic to build the +reverse-direction liftOver/quickLift chain, without re-aligning. +Each completed run also leaves (or refreshes) a dateless symlink +miniMap2.\$ToDb -> the dated build directory (miniMap2.\$fromDb.swap for a +-swap run), so later runs/tools can find \"the\" build for a pair without +knowing its date. All operations are performed in the build directory, which defaults to $HgAutomate::clusterData/\$fromDb/$HgAutomate::trackBuild/miniMap2\$ToDb.\$date for a plain UCSC database \$fromDb, or to .../asmHubs/{genbankBuild,refseqBuild}/GCx/ddd/ddd/ddd/<asmId>/trackData/miniMap2\$ToDb.\$date when \$fromDb is a GenArk accession (matching how pairwise lastz builds are organized under GenArk) -- unless -buildDir is given. "; # Detailed help (-help): print STDERR " Assumptions: 1. /scratch/data/\$db/\$db.2bit contains sequence for database/assembly \$db. 2. $HgAutomate::clusterData/\$db/chrom.sizes contains all sequence names and sizes from \$db.2bit. 3. The \$db.2bit files have already been distributed to cluster-scratch (/scratch/data/<db>/). 4. pafToPsl is on \$PATH on the machine that runs the align cluster jobs. 5. mash is on \$PATH on the machine that runs this script (used once, up front, to auto-select -minimapPreset unless it is given explicitly). 6. fromDb and toDb are two haplotypes/assemblies of the same species/ individual -- this is not a general any-vs-any pipeline. For that, use doBlastzChainNet.pl. " if ($detailed); print "\n"; exit $status; } # Globals: # Command line args: tDb=fromDb, qDb=toDb my ($tDb, $qDb); # Other: my ($buildDir); my ($tSeq, $tSizes, $qSeq, $qSizes, $QDb, $fileServer); -my ($liftOverChainDir, $liftOverChainFile, $liftOverChainPath); +my ($liftOverChainDir, $liftOverChainFile, $liftOverChainPath, $swapDir); sub checkOptions { # Make sure command line options are valid/supported. my $ok = GetOptions(@HgStepManager::optionSpec, 'buildDir=s', 'target2Bit=s', 'targetSizes=s', 'query2Bit=s', 'querySizes=s', 'minimapPreset=s', 'minimapCpu=i', 'minimapSecondaryN=i', 'minimapSecondaryRatio=f', 'chainRam=s', 'chainCpu=i', 'regenerateMash', + 'swap', + 'swapDir=s', @HgAutomate::commonOptionSpec, ); &usage(1) if (!$ok); &usage(0, 1) if ($opt_help); &HgAutomate::processCommonOptions(); my $err = $stepper->processOptions(); usage(1) if ($err); $dbHost = $opt_dbHost if ($opt_dbHost); if ($opt_minimapPreset) { $minimapPreset = $opt_minimapPreset; if ($minimapPreset !~ /^asm(5|10|20)$/) { die "-minimapPreset must be one of asm5, asm10, asm20 (got '$minimapPreset')\n"; } } # else: leave $minimapPreset undef -- estimateDivergence() will set it # from a mash distance once $tSeq/$qSeq/$buildDir are known. } sub getClusterSeqs { # Choose cluster and look for already-installed 2bit files on appropriate # cluster-scratch storage. Exit with an error message if we can't find them. my $paraHub = $opt_bigClusterHub ? $opt_bigClusterHub : &HgAutomate::chooseClusterByBandwidth(); my ($tSeqScratch, $qSeqScratch); if ($opt_target2Bit) { $tSeqScratch = $opt_target2Bit } else { my @okFilesystems = &HgAutomate::chooseFilesystemsForCluster($paraHub, 'in'); if ( -e "/scratch/data/$tDb/$tDb.2bit" ) { $tSeqScratch = "/scratch/data/$tDb/$tDb.2bit"; } else { foreach my $fs (@okFilesystems) { &HgAutomate::verbose(1, "checking $fs/$tDb/$tDb.2bit\n"); if (&HgAutomate::machineHasFile($paraHub, "$fs/$tDb/$tDb.2bit")) { $tSeqScratch = "$fs/$tDb/$tDb.2bit"; last; } } } if (! defined $tSeqScratch) { # No pre-staged cluster-scratch copy -- fall back to $tSeq, already # resolved by getSeqAndSizes() (GenArk build tree or clusterData), # which every cluster node can also reach, just not as fast as true # scratch storage: &HgAutomate::verbose(1, "align: no cluster-scratch copy of $tDb/$tDb.2bit found in " . join("/, ", @okFilesystems) . "/ -- using $tSeq instead.\n"); $tSeqScratch = $tSeq; } } if ($opt_query2Bit) { $qSeqScratch = $opt_query2Bit; } else { my @okFilesystems = &HgAutomate::chooseFilesystemsForCluster($paraHub, 'in'); if ( -e "/scratch/data/$qDb/$qDb.2bit" ) { $qSeqScratch = "/scratch/data/$qDb/$qDb.2bit"; } else { foreach my $fs (@okFilesystems) { if (&HgAutomate::machineHasFile($paraHub, "$fs/$qDb/$qDb.2bit")) { $qSeqScratch = "$fs/$qDb/$qDb.2bit"; last; } } } if (! defined $qSeqScratch) { # Same fallback as the target side above: &HgAutomate::verbose(1, "align: no cluster-scratch copy of $qDb/$qDb.2bit found in " . join("/, ", @okFilesystems) . "/ -- using $qSeq instead.\n"); $qSeqScratch = $qSeq; } } &HgAutomate::verbose(1, "Using $paraHub, $tSeqScratch and $qSeqScratch\n"); return ($paraHub, $tSeqScratch, $qSeqScratch); } # getClusterSeqs ######################################################################### # * step: align [bigClusterHub] sub doAlign { my $runDir = "$buildDir/run.mm2"; &HgAutomate::mustMkdir($runDir); my $pafDir = "$runDir/paf"; &HgAutomate::checkCleanSlate('align', 'chain', $pafDir, 'run.time'); my ($paraHub, $tSeqScratch, $qSeqScratch) = &getClusterSeqs(); # Unlike blat -fastMap, minimap2 does not need the query pre-split into # small chunks or an .ooc repeat mask -- it indexes and aligns whole # sequences directly. We only partition on the target side, one job # per target sequence (same trick doSameSpeciesLiftOver.pl uses: pick a # chunkSize at least as large as the biggest target sequence so nothing # actually gets split), and align each target job against the *whole* # query genome in one shot. # script for a single job: convert target 2bit spec(s) to fasta, align # against the pre-built whole-query fasta, convert PAF -> PSL. # NOTE: partitionSequence.pl may bundle several small target sequences # into one $runDir/tParts/partNNN.lst file instead of handing us a bare # 2bit spec directly (it does this whenever a genome has lots of tiny # scaffolds -- see its own usage message) -- path1 in that case is a # *relative* path like "tParts/part010.lst", so it has to be resolved # against $runDir before we cd elsewhere, and expanded into one # twoBitToFa call per line rather than treated as a single 2bit spec. my $fh = &HgAutomate::mustOpen(">$runDir/job.sh"); print $fh <<_EOF_ #!/bin/bash set -beEu -o pipefail targetSpec=\$1 outPsl=\$2 if [[ "\$targetSpec" == *.lst ]]; then targetSpec="$runDir/\$targetSpec" fi unset TMPDIR if [ -d "/data/tmp" ]; then export TMPDIR="/data/tmp" elif [ -d "/scratch/tmp" ]; then export TMPDIR="/scratch/tmp" else tmpSz=`df --output=avail -k /tmp | tail -1` shmSz=`df --output=avail -k /dev/shm | tail -1` if [ "\$shmSz" -gt "\$tmpSz" ]; then mkdir -p /dev/shm/tmp chmod 777 /dev/shm/tmp export TMPDIR="/dev/shm/tmp" else export TMPDIR="/tmp" fi fi # Use local disk for output, and move the final result to \$outPsl # when done, to minimize I/O. tmpDir=`mktemp -d -p \$TMPDIR doMm2.XXXXXX` pushd \$tmpDir > /dev/null : > target.fa if [[ "\$targetSpec" == *.lst ]]; then while read -r spec; do twoBitToFa "\$spec" stdout done < "\$targetSpec" > target.fa else twoBitToFa \$targetSpec target.fa fi minimap2 -cx $minimapPreset -N $minimapSecondaryN -p $minimapSecondaryRatio -t $minimapCpu \\ target.fa $runDir/query.fa > tmpOut.paf pafToPsl -tSizes=$tSizes -qSizes=$qSizes tmpOut.paf tmpOut.psl mv tmpOut.psl \$outPsl popd > /dev/null rm -rf \$tmpDir _EOF_ ; close($fh); &HgAutomate::run("chmod a+x $runDir/job.sh"); &HgAutomate::makeGsub($runDir, 'job.sh $(path1) {check out line ' . $pafDir . '/$(file1).psl}'); my $paraRun = &HgAutomate::paraRun($ramG, $minimapCpu); my $whatItDoes = "It performs a cluster run of minimap2 -cx $minimapPreset."; my $bossScript = newBash HgRemoteScript("$runDir/doAlign.bash", $paraHub, $runDir, $whatItDoes); # Don't allow target sequences to be split -- we align (and chain) whole # target sequences against the whole query, we never lift target coords # back up. Use the max target seq size as the chunkSize for # partitionSequence.pl on the target. my $tpSize = `awk '{print \$2;}' $tSizes | sort -nr | head -1`; chomp $tpSize; my $minTpSize = 10000000; $tpSize = $minTpSize if ($tpSize < $minTpSize); my $gensub2 = &HgAutomate::gensub2(); $bossScript->add(<<_EOF_ # Record how the preset was chosen (mash distance, if it ran -- see # estimateDivergence()) and exactly which minimap2 and what arguments were # used, for reproducibility -- the per-job command line is otherwise # buried in job.sh on whatever cluster node happened to run it. if [ -s $buildDir/mashDistance.txt ]; then cat $buildDir/mashDistance.txt > $buildDir/version.txt else printf "minimapPreset=$minimapPreset (explicit -minimapPreset, mash not run)\\n" > $buildDir/version.txt fi printf "minimap2 " >> $buildDir/version.txt minimap2 --version >> $buildDir/version.txt printf "minimap2 -cx $minimapPreset -N $minimapSecondaryN -p $minimapSecondaryRatio -t $minimapCpu target.fa query.fa > out.paf\\n" >> $buildDir/version.txt # Convert the whole query 2bit to fasta once; every target job aligns # against this same file. twoBitToFa $qSeqScratch query.fa # Compute partition (coordinate ranges) for cluster job. This does # not need to be run on the build fileserver because it does not actually # split any sequences -- it merely computes ranges based on the chrom.sizes. rm -rf tParts $Bin/partitionSequence.pl $tpSize 0 $tSeqScratch \\ $tSizes 2000 \\ -lstDir=tParts > t.lst mkdir $pafDir $gensub2 t.lst single gsub jobList $paraRun _EOF_ ); $bossScript->execute(); } # doAlign ######################################################################### # * step: chain [smallClusterHub] sub doChain { my $runDir = "$buildDir/axtChain/run"; &HgAutomate::mustMkdir($runDir); my $pafDir = "$buildDir/run.mm2/paf"; my $mm2DoneFile = "$buildDir/run.mm2/run.time"; &HgAutomate::checkCleanSlate('chain', 'net', 'chainRaw'); &HgAutomate::checkExistsUnlessDebug('align', 'chain', $pafDir, $mm2DoneFile); my ($paraHub, $tSeqScratch, $qSeqScratch) = &getClusterSeqs(); # One PSL per target sequence already (align step did not split further), # so the chain job list is simply the contents of $pafDir/*.psl. &HgAutomate::run("ls $pafDir/*.psl | xargs -n 1 basename > $runDir/pslParts.lst"); # script for a single job: chain one target-sequence's PSL. my $fh = &HgAutomate::mustOpen(">$runDir/job.sh"); print $fh <<_EOF_ #!/bin/bash set -beEu -o pipefail inPsl=\$1 outChain=\$2 unset TMPDIR if [ -d "/data/tmp" ]; then export TMPDIR="/data/tmp" elif [ -d "/scratch/tmp" ]; then export TMPDIR="/scratch/tmp" else tmpSz=`df --output=avail -k /tmp | tail -1` shmSz=`df --output=avail -k /dev/shm | tail -1` if [ "\$shmSz" -gt "\$tmpSz" ]; then mkdir -p /dev/shm/tmp chmod 777 /dev/shm/tmp export TMPDIR="/dev/shm/tmp" else export TMPDIR="/tmp" fi fi tmpOut=`mktemp -p \$TMPDIR doMm2.chain.XXXXXX` axtChain -verbose=0 -linearGap=medium -psl $pafDir/\$inPsl \\ $tSeqScratch $qSeqScratch stdout \\ | chainBridge -linearGap=medium stdin $tSeqScratch $qSeqScratch \\ \$tmpOut mv \$tmpOut \$outChain chmod 664 \$outChain _EOF_ ; close($fh); &HgAutomate::run("chmod a+x $runDir/job.sh"); &HgAutomate::makeGsub($runDir, 'job.sh $(path1) ' . '{check out line+ chainRaw/$(path1).chain}'); my $whatItDoes = "It does a cluster run to chain the minimap2 alignments."; my $bossScript = newBash HgRemoteScript("$runDir/doChain.bash", $paraHub, $runDir, $whatItDoes); my $paraRun = &HgAutomate::paraRun($chainRam, $chainCpu); my $gensub2 = &HgAutomate::gensub2(); $bossScript->add(<<_EOF_ mkdir chainRaw $gensub2 pslParts.lst single gsub jobList $paraRun _EOF_ ); $bossScript->execute(); } # doChain +######################################################################### +# netFromChainBash($chainPath, $tSz, $qSz, $outDir, $overFile, $tName, $qName) +# -> bash source (string) that nets a single, already merge-sorted chain +# file into a liftOver chain + quickLift chain pair. $chainPath can be +# a literal path or a not-yet-Perl-interpolated bash expression (the +# caller controls that by how it quotes the argument) -- this doesn't +# care, it just emits it verbatim. Shared by doNet() (on the freshly +# merged chainRaw/*.chain) and doSwap() (on a chainSwap'd chain) so the +# "net one chain" logic isn't duplicated between them. +sub netFromChainBash { + my ($chainPath, $tSz, $qSz, $outDir, $overFile, $tName, $qName) = @_; + return <<_EOF_ +chainNet $chainPath \\ + $tSz $qSz \\ + noClass.net /dev/null +netChainSubset noClass.net $chainPath stdout \\ +| chainStitchId stdin stdout | gzip -c > $outDir/$overFile + +# make quickLift chain: +chainSwap $outDir/$overFile stdout \\ + | chainToBigChain stdin $outDir/$tName.$qName.quick.chain.txt \\ + $outDir/$tName.$qName.quick.link.txt +_EOF_ + ; +} # netFromChainBash + ######################################################################### # * step: net [workhorse] sub doNet { my $runDir = "$buildDir/axtChain"; my @outs = ("$runDir/$tDb.$qDb.all.chain.gz", "$runDir/noClass.net"); &HgAutomate::checkCleanSlate('net', 'load', @outs); &HgAutomate::checkExistsUnlessDebug('chain', 'net', "$runDir/run/chainRaw/"); my $whatItDoes = "It nets the chained minimap2 alignments and runs netChainSubset to produce liftOver chains."; my $mach = &HgAutomate::chooseWorkhorse(); my $bossScript = newBash HgRemoteScript("$runDir/doNet.bash", $mach, $runDir, $whatItDoes); - my $chromBased = (`wc -l < $tSizes` <= $HgAutomate::splitThreshold); - my $lump = $chromBased ? "" : "-lump=100"; $bossScript->add(<<_EOF_ unset TMPDIR if [ -d "/data/tmp" ]; then export TMPDIR="/data/tmp" elif [ -d "/scratch/tmp" ]; then export TMPDIR="/scratch/tmp" else tmpSz=`df --output=avail -k /tmp | tail -1` shmSz=`df --output=avail -k /dev/shm | tail -1` if [ "\$shmSz" -gt "\$tmpSz" ]; then mkdir -p /dev/shm/tmp chmod 777 /dev/shm/tmp export TMPDIR="/dev/shm/tmp" else export TMPDIR="/tmp" fi fi -# Use local scratch disk... this can be quite I/O intensive: tmpDir=`mktemp -d -p \$TMPDIR doMm2.net.XXXXXX` -# Merge up the hierarchy and assign unique chain IDs: -chainMergeSort run/chainRaw/*.chain \\ -| chainSplit $lump \$tmpDir/chainSplit stdin -endsInLf \$tmpDir/chainSplit/*.chain - -mkdir \$tmpDir/netSplit \$tmpDir/overSplit -for f in \$tmpDir/chainSplit/*.chain; do - split=\$(basename "\$f" .chain) - chainNet \$f \\ - $tSizes $qSizes \\ - \$tmpDir/netSplit/\$split.net /dev/null - netChainSubset \$tmpDir/netSplit/\$split.net \$f stdout \\ - | chainStitchId stdin \$tmpDir/overSplit/\$split.chain -done -endsInLf \$tmpDir/netSplit/*.net -endsInLf \$tmpDir/overSplit/*.chain - -cat \$tmpDir/chainSplit/*.chain | gzip -c > $tDb.$qDb.all.chain.gz -# noClass.net is scaffolding for netChainSubset above, not a kept product -# (matches doBlastzChainNet.pl's own treatment -- see cleanup step): -cat \$tmpDir/netSplit/*.net > noClass.net - -cat \$tmpDir/overSplit/*.chain | gzip -c > $runDir/$liftOverChainFile -# make quickLift chain: -chainSwap $runDir/$liftOverChainFile stdout \\ - | chainToBigChain stdin $runDir/$tDb.$qDb.quick.chain.txt \\ - $runDir/$tDb.$qDb.quick.link.txt +# Merge up the hierarchy and assign unique chain IDs -- one chain file for +# the whole genome. chainNet doesn't need this pre-split by chromosome +# the way doSameSpeciesLiftOver.pl split it; that was only ever a scale +# optimization doBlastzChainNet.pl itself only applies conditionally (its +# own \$splitRef), and this same-species/haplotype-scale pipeline doesn't +# need it either. +chainMergeSort run/chainRaw/*.chain > \$tmpDir/all.chain +gzip -c \$tmpDir/all.chain > $tDb.$qDb.all.chain.gz +_EOF_ + ); + $bossScript->add(&netFromChainBash('$tmpDir/all.chain', $tSizes, $qSizes, + $runDir, $liftOverChainFile, $tDb, $qDb)); + $bossScript->add(<<_EOF_ rm -rf \$tmpDir/ _EOF_ ); $bossScript->execute(); } # doNet ######################################################################### # * step: load [dbHost] sub doLoad { my $runDir = "$buildDir/axtChain"; &HgAutomate::checkExistsUnlessDebug('net', 'load', "$runDir/$liftOverChainFile"); my $whatItDoes = "It builds the chain/chainLiftOver/quickLift bigBed pairs, links them into $HgAutomate::gbdb/ (GenArk hub-build/accession chain, or native db layout -- see installLinks() in ottoRequestWatch.sh, which this mirrors), and calls hgAddLiftOverChain + addQuickLift.py to register both in hgcentral. None of this needs \$tDb to be a real MySQL database -- hgAddLiftOverChain and addQuickLift.py both work fine with obsolete/nonexistent ones by design (see hgAddLiftOverChain.c's own comment to that effect)."; my $bossScript = newBash HgRemoteScript("$runDir/doLoad.bash", $dbHost, $runDir, $whatItDoes); $bossScript->add(<<_EOF_ 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' # Full-chain bigChain pair, from the complete alignment (all.chain.gz) -- # the standard genome-browser Chain/Net-style track pair. Built for any # target/query pair -- nothing about this needs \$tDb to be a real # database, only \$tSizes and the chain files doNet already produced. hgLoadChain -test -noBin -tIndex $tDb chain$QDb $runDir/$tDb.$qDb.all.chain.gz sed 's/.000000//' chain.tab | awk 'BEGIN {OFS="\\t"} {print \$2, \$4, \$5, \$11, 1000, \$8, \$3, \$6, \$7, \$9, \$10, \$1}' > chain${QDb}.tab bedToBigBed -type=bed6+6 -as=bigChain.as -tab chain${QDb}.tab $tSizes chain${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 $tSizes chain${QDb}Link.bb totalBases=`ave -col=2 $tSizes | grep "^total" | awk '{printf "%d", \$2}'` basesCovered=`bigBedInfo chain${QDb}Link.bb | grep "basesCovered" | cut -d' ' -f2 | tr -d ','` percentCovered=`echo \$basesCovered \$totalBases | awk '{printf "%.3f", 100.0*\$1/\$2}'` printf "%d bases of %d (%s%%) in intersection\\n" "\$basesCovered" "\$totalBases" "\$percentCovered" > $buildDir/fb.$tDb.chain${QDb}Link.txt rm -f link.tab chain.tab chain${QDb}.tab chain${QDb}Link.tab # LiftOver-subset bigChain pair, from the netChainSubset-extracted chain # (over.chain.gz) -- the strict, single-best-path-per-region subset. # Also built unconditionally, same reasoning as above. hgLoadChain -test -noBin -tIndex $tDb chainLiftOver$QDb $runDir/$liftOverChainFile 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 $tSizes chainLiftOver${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 $tSizes chainLiftOver${QDb}Link.bb liftOverBasesCovered=`bigBedInfo chainLiftOver${QDb}Link.bb | grep "basesCovered" | cut -d' ' -f2 | tr -d ','` liftOverPercentCovered=`echo \$liftOverBasesCovered \$totalBases | awk '{printf "%.3f", 100.0*\$1/\$2}'` printf "%d bases of %d (%s%%) in intersection\\n" "\$liftOverBasesCovered" "\$totalBases" "\$liftOverPercentCovered" > $buildDir/fb.$tDb.chainLiftOver${QDb}.txt rm -f link.tab chain.tab chainLiftOver${QDb}.tab chainLiftOver${QDb}Link.tab _EOF_ ); # Where the liftOver chain / quickLift bigBeds get linked, and what gets # registered in hgcentral, depends only on whether $tDb LOOKS like a # GenArk accession (a plain name-pattern check, same as everywhere else # in this pipeline) -- never on whether it's a real MySQL database. # This mirrors ottoRequestWatch.sh's installLinks() exactly, except # resolving the GenArk build directory via genbankBuild/refseqBuild # (AsmHub::asmBuildDir(), verified against the real on-disk layout) # rather than the allBuild path installLinks() itself uses. my $tAccession = &accessionFromPath($tDb); if ($tAccession) { my $tBuildDir = &asmBuildDir($tAccession); die "doLoad: '$tDb' looks like a GenArk accession, but no build " . "directory was found for it under $HgAutomate::clusterData/asmHubs/\n" if (! $tBuildDir); my $accessionPath = &asmIdToPath($tAccession) . "/$tAccession"; my $accLevelDir = "$HgAutomate::clusterData/asmHubs/$accessionPath"; my $gbdbGenarkDir = "/gbdb/genark/$accessionPath"; $bossScript->add(<<_EOF_ # GenArk assembly: link into the hub-build directory, then the # accession-level convenience symlinks, then the public gbdb symlinks -- # same three-tier chain installLinks() uses. mkdir -p $tBuildDir/liftOver $tBuildDir/quickLift rm -f $tBuildDir/liftOver/$liftOverChainFile ln -s $runDir/$liftOverChainFile $tBuildDir/liftOver/$liftOverChainFile rm -f $tBuildDir/quickLift/$qDb.bb $tBuildDir/quickLift/$qDb.link.bb ln -s $runDir/$tDb.$qDb.quick.bb $tBuildDir/quickLift/$qDb.bb ln -s $runDir/$tDb.$qDb.quickLink.bb $tBuildDir/quickLift/$qDb.link.bb mkdir -p $accLevelDir rm -f $accLevelDir/liftOver $accLevelDir/quickLift ln -s $tBuildDir/liftOver $accLevelDir/liftOver ln -s $tBuildDir/quickLift $accLevelDir/quickLift mkdir -p $gbdbGenarkDir rm -f $gbdbGenarkDir/liftOver $gbdbGenarkDir/quickLift ln -s $accLevelDir/liftOver $gbdbGenarkDir/liftOver ln -s $accLevelDir/quickLift $gbdbGenarkDir/quickLift # Register in hgcentral (works fine without a real MySQL database for # \$tDb -- see hgAddLiftOverChain.c and addQuickLift.py): hgAddLiftOverChain -minMatch=0.1 -multiple -path=$gbdbGenarkDir/liftOver/$liftOverChainFile $tDb $qDb $Bin/addQuickLift.py $tDb $qDb $gbdbGenarkDir/quickLift/$qDb.bb _EOF_ ); } else { $bossScript->add(<<_EOF_ # Not a GenArk accession -- native-db-style layout (same as # installLinks()'s native-db branch), whether or not \$tDb is actually a # real MySQL database (e.g. hs1: a full sequence build, no database). mkdir -p $liftOverChainDir rm -f $liftOverChainPath ln -s $runDir/$liftOverChainFile $liftOverChainPath tmpFile=`mktemp -t -p /tmp tmpMd5.XXXXXX` grep -v $liftOverChainFile $liftOverChainDir/md5sum.txt > \$tmpFile || true md5sum $runDir/$liftOverChainFile | sed -e "s#$runDir/##;" >> \$tmpFile sort \$tmpFile > $liftOverChainDir/md5sum.txt rm -f \$tmpFile # Link from download area: mkdir -p $HgAutomate::goldenPath/$tDb/liftOver rm -f $HgAutomate::goldenPath/$tDb/liftOver/$liftOverChainFile ln -s $liftOverChainPath $HgAutomate::goldenPath/$tDb/liftOver/ # Link from genome browser fileserver: mkdir -p $HgAutomate::gbdb/$tDb/liftOver $HgAutomate::gbdb/$tDb/quickLift rm -f $HgAutomate::gbdb/$tDb/liftOver/$liftOverChainFile ln -s $liftOverChainPath $HgAutomate::gbdb/$tDb/liftOver/ rm -f $HgAutomate::gbdb/$tDb/quickLift/$qDb.bb $HgAutomate::gbdb/$tDb/quickLift/$qDb.link.bb ln -s $runDir/$tDb.$qDb.quick.bb $HgAutomate::gbdb/$tDb/quickLift/$qDb.bb ln -s $runDir/$tDb.$qDb.quickLink.bb $HgAutomate::gbdb/$tDb/quickLift/$qDb.link.bb # Register in hgcentral (works fine without a real MySQL database for # \$tDb -- see hgAddLiftOverChain.c and addQuickLift.py): hgAddLiftOverChain -minMatch=0.1 -multiple -path=$HgAutomate::gbdb/$tDb/liftOver/$liftOverChainFile $tDb $qDb $Bin/addQuickLift.py $tDb $qDb $HgAutomate::gbdb/$tDb/quickLift/$qDb.bb _EOF_ ); } # quickLift bigBed pair: built for any target/query pair -- it only # needs the quick.chain.txt/quick.link.txt doNet already produced, # plus $qSizes, no dependency on \$tDb being a real database. $bossScript->add(<<_EOF_ bedToBigBed -type=bed6+6 -as=bigChain.as -tab $tDb.$qDb.quick.chain.txt $qSizes $tDb.$qDb.quick.bb bedToBigBed -type=bed4+1 -as=bigLink.as -tab $tDb.$qDb.quick.link.txt $qSizes $tDb.$qDb.quickLink.bb qBases=`ave -col=2 $qSizes | grep "^total" | awk '{printf "%d", \$2}'` qCovered=`bigBedInfo $tDb.$qDb.quickLink.bb | grep "basesCovered" | cut -d' ' -f2 | tr -d ','` qPerCent=`echo \$qCovered \$qBases | awk '{printf "%.3f", 100.0*\$1/\$2}'` printf "%d bases of %d (%s%%) in intersection\\n" "\$qCovered" "\$qBases" "\$qPerCent" > $buildDir/fb.$tDb.quick${QDb}Link.txt rm -f bigChain.as bigLink.as $tDb.$qDb.quick.chain.txt $tDb.$qDb.quick.link.txt _EOF_ ); $bossScript->execute(); } # doLoad +######################################################################### +# swapGlobals: swap $tDb/$qDb (and everything derived from them) so +# doLoad() can be reused unchanged for the -swap direction, mirroring +# doBlastzChainNet.pl's own swapGlobals(). $buildDir becomes $swapDir, +# which the caller (doSwap()) must have already set. +sub swapGlobals { + ($tDb, $qDb) = ($qDb, $tDb); + $QDb = ucfirst($qDb); + ($tSeq, $qSeq) = ($qSeq, $tSeq); + ($tSizes, $qSizes) = ($qSizes, $tSizes); + $buildDir = $swapDir; + $liftOverChainDir = "$HgAutomate::clusterData/$tDb/$HgAutomate::trackBuild/liftOver"; + $liftOverChainFile = "${tDb}To${QDb}.over.chain.gz"; + $liftOverChainPath = "$liftOverChainDir/$liftOverChainFile"; +} # swapGlobals + +######################################################################### +# * -swap (not a normal stepper step): chainSwap the primary run's +# all.chain.gz and reuse doNet()'s netFromChainBash() + doLoad() to +# produce the reverse-direction liftOver/quickLift chain, without +# re-aligning anything. +sub doSwap { + my $origTDb = $tDb; + my $origQDb = $qDb; + + my $primaryChain = "$buildDir/axtChain/$origTDb.$origQDb.all.chain.gz"; + if (! -e $primaryChain) { + die "-swap: can't find $primaryChain -- run the primary $origTDb " . + "$origQDb build (through at least the 'net' step) first.\n"; + } + + $swapDir = $opt_swapDir ? $opt_swapDir : + &asmRoot($origQDb) . "/miniMap2.$origTDb.swap"; + my $runDir = "$swapDir/axtChain"; + &HgAutomate::mustMkdir($runDir); + + my $whatItDoes = +"It chainSwaps the primary $origTDb/$origQDb run's all.chain.gz and nets it +to produce the $origQDb-to-$origTDb liftOver/quickLift chain, without +re-aligning."; + my $mach = &HgAutomate::chooseWorkhorse(); + my $bossScript = newBash HgRemoteScript("$runDir/doSwap.bash", $mach, + $runDir, $whatItDoes); + + my $swappedOver = "${origQDb}To" . ucfirst($origTDb) . ".over.chain.gz"; + $bossScript->add(<<_EOF_ +unset TMPDIR +if [ -d "/data/tmp" ]; then + export TMPDIR="/data/tmp" +elif [ -d "/scratch/tmp" ]; then + export TMPDIR="/scratch/tmp" +else + tmpSz=`df --output=avail -k /tmp | tail -1` + shmSz=`df --output=avail -k /dev/shm | tail -1` + if [ "\$shmSz" -gt "\$tmpSz" ]; then + mkdir -p /dev/shm/tmp + chmod 777 /dev/shm/tmp + export TMPDIR="/dev/shm/tmp" + else + export TMPDIR="/tmp" + fi +fi +tmpDir=`mktemp -d -p \$TMPDIR doMm2.swap.XXXXXX` + +# chainSwap flips target/query coordinates on each already uniquely-ID'd +# chain block; chainSort re-sorts by the new target's coordinate order, +# same as doBlastzChainNet.pl's own swapChains() -- no need to re-run +# chainMergeSort, the IDs from the primary run are still unique. +chainSwap $primaryChain stdout | chainSort stdin \$tmpDir/all.chain +gzip -c \$tmpDir/all.chain > $origQDb.$origTDb.all.chain.gz + +_EOF_ + ); + $bossScript->add(&netFromChainBash('$tmpDir/all.chain', $qSizes, $tSizes, + $runDir, $swappedOver, $origQDb, $origTDb)); + $bossScript->add(<<_EOF_ +rm -rf \$tmpDir/ +_EOF_ + ); + $bossScript->execute(); + + # Reuse doLoad() unchanged for the swapped direction -- swapGlobals() + # makes it think it's doing a normal, primary $origQDb-to-$origTDb run: + &swapGlobals(); + &doLoad(); + + # Stable, dateless pointer to this swap build, in $origQDb's own root + # (relative target, so it stays correct if this tree gets mirrored): + my $swapBase = basename($swapDir); + my $stableLink = &asmRoot($origQDb) . "/miniMap2.$origTDb"; + &HgAutomate::run("rm -f $stableLink"); + &HgAutomate::run("ln -s $swapBase $stableLink"); +} # doSwap + + ######################################################################### # * step: cleanup [fileServer] sub doCleanup { my $runDir = "$buildDir"; my $whatItDoes = "It cleans up or compresses intermediate files."; $fileServer = &HgAutomate::chooseFileServer($runDir); my $bossScript = newBash HgRemoteScript("$runDir/doCleanup.bash", $fileServer, $runDir, $whatItDoes); $bossScript->add(<<_EOF_ rm -f run.mm2/query.fa rm -rf run.mm2/paf/ rm -rf axtChain/run/chainRaw/ rm -f axtChain/noClass.net # mashSketch.{a,b}.msh only ever exist here if estimateDivergence() fell # back to a one-off sketch (tSeq/qSeq didn't resolve to a real GenArk # accession or UCSC db -- see AssemblyDivergence.pm's sketch()); for a # normal assembly the sketch lives in its own permanent, shared cache # under /hive/data/genomes/, never here, so this is a no-op in that case: rm -f mashSketch.a.msh mashSketch.b.msh _EOF_ ); $bossScript->execute(); } # doCleanup +# asmRoot($db) -> this assembly's own build-directory root: +# a GenArk accession's real build dir + "/trackData" (matching how +# pairwise lastz builds are organized under GenArk), or +# clusterData/$db/$HgAutomate::trackBuild for a plain UCSC database. +# Used for both $buildDir (rooted at $tDb) and $swapDir (rooted at +# $qDb), and for where each run's dateless "current build" symlink goes. +sub asmRoot { + my ($db) = @_; + my $accession = &accessionFromPath($db); + my $asmBuild = $accession ? &asmBuildDir($accession) : undef; + return $asmBuild ? "$asmBuild/trackData" + : "$HgAutomate::clusterData/$db/$HgAutomate::trackBuild"; +} # asmRoot + # resolveAssemblySeq($db, $opt2Bit, $optSizes) -> ($seq, $sizes) # $opt2Bit/$optSizes, if given (-target2Bit etc.), always win. # Otherwise, if $db looks like a GenArk accession (accessionFromPath()) # with a real build directory (AsmHub::asmBuildDir()), resolve straight # to that build tree's own <asmId>.2bit/.chrom.sizes -- the same # resolution AssemblyDivergence.pm's sketch() already does for mash, # just for the actual alignment inputs here. Otherwise falls back to # the traditional /scratch/data or clusterData/$db/$db.2bit UCSC-db # location, as before. Doesn't require the result to actually exist -- # getSeqAndSizes() checks that afterward. sub resolveAssemblySeq { my ($db, $opt2Bit, $optSizes) = @_; my $accession = &accessionFromPath($db); my $asmBuild = $accession ? &asmBuildDir($accession) : undef; my $asmId = $asmBuild ? basename($asmBuild) : undef; my $seq; if ($opt2Bit) { $seq = $opt2Bit; } elsif ($asmBuild) { $seq = "$asmBuild/$asmId.2bit"; } else { $seq = "/scratch/data/$db/$db.2bit"; if (! -e $seq) { # allow it to exist here too: my $fs = "$HgAutomate::clusterData"; &HgAutomate::verbose(1, "checking $fs/$db/$db.2bit\n"); $seq = "$fs/$db/$db.2bit" if (-e "$fs/$db/$db.2bit"); } } my $sizes; if ($optSizes) { $sizes = $optSizes; } elsif ($asmBuild) { $sizes = "$asmBuild/$asmId.chrom.sizes"; } else { $sizes = "$HgAutomate::clusterData/$db/chrom.sizes"; } return ($seq, $sizes); } # resolveAssemblySeq sub getSeqAndSizes { ($tSeq, $tSizes) = &resolveAssemblySeq($tDb, $opt_target2Bit, $opt_targetSizes); ($qSeq, $qSizes) = &resolveAssemblySeq($qDb, $opt_query2Bit, $opt_querySizes); my $problem = 0; foreach my $file ($tSeq, $tSizes, $qSeq, $qSizes) { if (! -e $file) { warn "Error: cannot find required file \"$file\"\n"; $problem = 1; } } if ($problem && !$opt_debug) { warn "Run $base -help for a description of expected files.\n"; exit 1; } } # getSeqAndSizes sub estimateDivergence { # Pick -minimapPreset automatically via AssemblyDivergence.pm's mash # distance between tDb and qDb, unless the user already gave # -minimapPreset explicitly. Cheap (mash sketch+dist on a whole genome # is seconds to low minutes), so we just run it locally rather than # turning it into its own cluster step. if ($minimapPreset) { &HgAutomate::verbose(1, "Using explicit -minimapPreset=$minimapPreset (mash not run).\n"); return; } my $mashFile = "$buildDir/mashDistance.txt"; if (-e $mashFile && ! $opt_regenerateMash) { # Reuse a previous estimate so -continue steps stay consistent with # whatever the align step (if already run) actually used. open(my $fh, "<", $mashFile) || die "Can't read $mashFile: $!\n"; my $line = <$fh>; close($fh); if ($line =~ /^mashDistance=(\S+)\s+minimapPreset=(\S+)/) { $minimapPreset = $2; &HgAutomate::verbose(1, "Reusing cached mash distance $1 -> " . "-minimapPreset=$minimapPreset from $mashFile\n"); return; } } if ($opt_debug) { $minimapPreset = 'asm5'; &HgAutomate::verbose(1, "-debug: skipping mash, using -minimapPreset=$minimapPreset\n"); return; } &HgAutomate::verbose(1, "Estimating $tDb/$qDb divergence with mash to pick -minimapPreset ...\n"); my $dist = eval { &AssemblyDivergence::mashDistance($tSeq, $qSeq, $buildDir, $opt_regenerateMash); }; if ($@) { $minimapPreset = 'asm5'; warn "estimateDivergence: $@" . "falling back to -minimapPreset=$minimapPreset. Pass " . "-minimapPreset explicitly to pick it yourself and silence this.\n"; return; } my ($pipeline, $preset, $warning) = &AssemblyDivergence::choosePipeline($dist); warn "$warning\n" if ($warning); if ($pipeline ne 'minimap2') { die "estimateDivergence: mash distance $dist between $tDb and $qDb " . "looks too diverged for doMiniMap2.pl -- use doBlastzChainNet.pl " . "instead, or re-run with -minimapPreset to force minimap2 anyway.\n"; } $minimapPreset = $preset; open(my $fh, ">", $mashFile) || die "Can't write $mashFile: $!\n"; print $fh "mashDistance=$dist minimapPreset=$minimapPreset\n"; close($fh); &HgAutomate::verbose(1, "mash distance $dist between $tDb and $qDb -> -minimapPreset=$minimapPreset\n"); } # estimateDivergence ######################################################################### # main # Prevent "Suspended (tty input)" hanging: &HgAutomate::closeStdin(); &checkOptions(); &usage(1) if (scalar(@ARGV) != 2); ($tDb, $qDb) = @ARGV; &getSeqAndSizes(); $QDb = ucfirst($qDb); $liftOverChainDir = "$HgAutomate::clusterData/$tDb/$HgAutomate::trackBuild/liftOver"; $liftOverChainFile = "${tDb}To${QDb}.over.chain.gz"; $liftOverChainPath = "$liftOverChainDir/$liftOverChainFile"; $chainRam = $opt_chainRam ? $opt_chainRam : $chainRam; $chainCpu = $opt_chainCpu ? $opt_chainCpu : $chainCpu; $minimapCpu = $opt_minimapCpu ? $opt_minimapCpu : $minimapCpu; $minimapSecondaryN = $opt_minimapSecondaryN ? $opt_minimapSecondaryN : $minimapSecondaryN; $minimapSecondaryRatio = $opt_minimapSecondaryRatio ? $opt_minimapSecondaryRatio : $minimapSecondaryRatio; $ramG = $opt_ram ? $opt_ram : $ramG; my $date = `date +%Y-%m-%d`; chomp $date; -if ($opt_buildDir) { - $buildDir = $opt_buildDir; -} else { - # GenArk target: build under its own trackData/, same convention - # ottoRequestWatch.sh expects pairwise lastz builds to already be in - # (".../<asmId>/trackData/lastz<Q>.YYYY-MM-DD") -- not under - # clusterData/$tDb/bed/, which only exists for native UCSC databases. - my $tAccession = &accessionFromPath($tDb); - my $tAsmBuild = $tAccession ? &asmBuildDir($tAccession) : undef; - $buildDir = $tAsmBuild ? - "$tAsmBuild/trackData/miniMap2${QDb}.$date" : - "$HgAutomate::clusterData/$tDb/$HgAutomate::trackBuild/miniMap2${QDb}.$date"; +$buildDir = $opt_buildDir ? $opt_buildDir : + &asmRoot($tDb) . "/miniMap2${QDb}.$date"; + +if ($opt_swap) { + # -swap reuses the primary run's already-completed axtChain/all.chain.gz + # (doSwap() checks for it directly) -- never auto-create $buildDir here. + if (! -d $buildDir) { + die "-swap: $buildDir does not exist -- run the primary $tDb $qDb " . + "build first, or give -buildDir to point at it.\n"; + } + &doSwap(); + &HgAutomate::verbose(1, + "\n *** All done! -swap steps were performed in $swapDir\n\n"); + exit 0; } if (! -d $buildDir) { if ($stepper->stepPrecedes('align', $stepper->getStartStep())) { die "$buildDir does not exist; try running again with -buildDir.\n"; } &HgAutomate::mustMkdir($buildDir); } &estimateDivergence(); $stepper->execute(); my $stopStep = $stepper->getStopStep(); my $upThrough = ($stopStep eq 'cleanup') ? "" : " (through the '$stopStep' step)"; +# Stable, dateless pointer to this build, refreshed on every run +# (relative target, so it stays correct if this tree gets mirrored): +my $stableLink = &asmRoot($tDb) . "/miniMap2.$QDb"; +&HgAutomate::run("rm -f $stableLink"); +&HgAutomate::run("ln -s " . basename($buildDir) . " $stableLink"); + &HgAutomate::verbose(1, "\n *** All done!$upThrough\n"); &HgAutomate::verbose(1, " *** Steps were performed in $buildDir\n"); if ($stepper->stepPrecedes('net', $stopStep)) { &HgAutomate::verbose(1, " *** Test installation ($HgAutomate::gbdb, goldenPath, hgLiftover " . "operation) on $dbHost.\n"); } &HgAutomate::verbose(1, "\n");