b5ae994376f6ea39fdca045b159a3cb942a36c82
hiram
  Wed Mar 6 21:40:27 2024 -0800
correct reference target for symlink of repeat modeler files to top level build dir no redmine

diff --git src/hg/utils/automation/doRepeatModeler.pl src/hg/utils/automation/doRepeatModeler.pl
index 42c0623..f993016 100755
--- src/hg/utils/automation/doRepeatModeler.pl
+++ src/hg/utils/automation/doRepeatModeler.pl
@@ -241,36 +241,36 @@
   }
   my $whatItDoes = "Cleans up or compresses intermediate files.";
   my $bossScript = newBash HgRemoteScript("$runDir/modelerCleanup.bash", $workhorse,
 				      $runDir, $whatItDoes);
   $bossScript->add(<<_EOF_
 export asmId="${db}"
 
 if [ ! -s "\${asmId}-families.fa" ]; then
   printf "cleanup expected result file: \${asmId}-families.fa does not exist\n" 1>&2
   exit 255
 fi
 rm -fr \${asmId}.fa \${asmId}.n?? ./err/
 if [ -s "\${asmId}-families.stk" ]; then
   gzip \${asmId}-families.stk
 fi
-rm -f ${buildDir}/\${asmId}.repeatModeler.families.stk.gz
-rm -f ${buildDir}/\${asmId}.rmod.log.txt
-ln -s trackData/repeatModeler/\${asmId}-families.stk ${buildDir}/\${asmId}.repeatModeler.families.stk.gz
-ln -s trackData/repeatModeler/\${asmId}-rmod.log ${buildDir}/\${asmId}.rmod.log.txt
-gzip -c "\${asmId}-families.fa" > "${buildDir}/\${asmId}.repeatModeler.families.fa.gz"
-touch -r "\${asmId}-families.fa" "${buildDir}/\${asmId}.repeatModeler.families.fa.gz"
+rm -f ${buildDir}/../../\${asmId}.repeatModeler.families.stk.gz
+rm -f ${buildDir}/../../\${asmId}.rmod.log.txt
+ln -s trackData/repeatModeler/\${asmId}-families.stk ${buildDir}/../../\${asmId}.repeatModeler.families.stk.gz
+ln -s trackData/repeatModeler/\${asmId}-rmod.log ${buildDir}/../../\${asmId}.rmod.log.txt
+gzip -c "\${asmId}-families.fa" > "${buildDir}/../../\${asmId}.repeatModeler.families.fa.gz"
+touch -r "\${asmId}-families.fa" "${buildDir}/../../\${asmId}.repeatModeler.families.fa.gz"
 c=`ls -d RM_* | wc -l`
 if [ "\${c}" -eq 1 ]; then
    RM_dir=`ls -d RM_*`
    if [ -d "\${RM_dir}" ]; then
      rm -fr "\${RM_dir}"
    else
      printf "directory RM_* not found ?\\n" 1>&2
      ls -d RM* 1>&2
      exit 255
    fi
 else
    printf "single directory RM_* not found ?\\n" 1>&2
    ls -d RM* 1>&2
    exit 255
 fi