8b71be65ac62a68201a8681bc3e7bce756011487 hiram Mon Mar 28 12:45:39 2022 -0700 correct symlink for chromAlias.bb refs #27228 diff --git src/hg/utils/automation/doAssemblyHub.pl src/hg/utils/automation/doAssemblyHub.pl index 408562d..5182c96 100755 --- src/hg/utils/automation/doAssemblyHub.pl +++ src/hg/utils/automation/doAssemblyHub.pl @@ -1924,31 +1924,32 @@ my $whatItDoes = "construct asmId.trackDb.txt file"; my $bossScript = newBash HgRemoteScript("$runDir/doTrackDb.bash", $workhorse, $runDir, $whatItDoes); if (! -s "${buildDir}/trackData/chromAlias/${asmId}.chromAlias.txt" ) { die "ERROR: can not find ${asmId}.chromAlias.txt in\n# ${buildDir}/trackData/chromAlias/\n"; } $bossScript->add(<<_EOF_ export asmId=$asmId export buildDir=$buildDir rm -f \$asmId.chromAlias.txt ln -s trackData/chromAlias/\${asmId}.chromAlias.txt . if [ -s trackData/chromAlias/\${asmId}.chromAlias.bb ]; then - ln -s -s trackData/chromAlias/\${asmId}.chromAlias.bb . + rm -f \${asmId}.chromAlias.bb + ln -s trackData/chromAlias/\${asmId}.chromAlias.bb . fi \$HOME/kent/src/hg/utils/automation/asmHubTrackDb.sh \$asmId \$buildDir \\ > \$asmId.trackDb.txt _EOF_ ); $bossScript->execute(); } # trackDb ######################################################################### # * step: cleanup [fileServer] sub doCleanup { my $runDir = "$buildDir"; my $whatItDoes = "clean up or compresses intermediate files."; my $bossScript = newBash HgRemoteScript("$runDir/doCleanup.bash", $fileServer,