590d349ae81a1ea322bc821c93f68652cde2d208
angie
  Thu May 7 09:41:02 2020 -0700
Make a safe directory for files linked from /gbdb, so gbdb links don't point to corrupted daily files when a rebuild gets an error.  refs #25188

diff --git src/hg/utils/otto/nextstrainNcov/doUpdate.sh src/hg/utils/otto/nextstrainNcov/doUpdate.sh
index 1b28d31..c0a8cbd 100755
--- src/hg/utils/otto/nextstrainNcov/doUpdate.sh
+++ src/hg/utils/otto/nextstrainNcov/doUpdate.sh
@@ -59,34 +59,42 @@
     nextstrainClade.bb
 
 bedToBigBed -type=bed4 -tab -verbose=0 nextstrainDiscarded.bed $chromSizes \
     nextstrainDiscarded.bb
 
 bedToBigBed -type=bed4 -tab -verbose=0 nextstrainBlacklisted.bed $chromSizes \
     nextstrainBlacklisted.bb
 
 bedToBigBed -type=bed4 -tab -verbose=0 nextstrainInformative.bed $chromSizes \
     nextstrainInformative.bb
 
 # bigWig for the tree parsimony scores track for David
 bedGraphToBigWig nextstrainParsimony.bedGraph $chromSizes nextstrainParsimony.bw
 
 # Install
-ln -sf $runDir/nextstrainGene.bb $runDir/nextstrainClade.bb \
+mkdir -p $ottoDir/current
+cp -pf $runDir/nextstrainGene.bb $runDir/nextstrainClade.bb \
     $runDir/nextstrain*.vcf.gz{,.tbi} \
     $runDir/nextstrain*.nh \
+    $ottoDir/current/
+ln -sf $ottoDir/current/nextstrainGene.bb $ottoDir/current/nextstrainClade.bb \
+    $ottoDir/current/nextstrain*.vcf.gz{,.tbi} \
+    $ottoDir/current/nextstrain*.nh \
     $gbdbDir/
 
 # Install but don't archive (for now) the experimental tracks for David.
-ln -sf $runDir/nextstrain{Discarded,Blacklisted,Informative}.bb \
+cp -pf $runDir/nextstrain{Discarded,Blacklisted,Informative}.bb \
     $runDir/nextstrainParsimony.bw \
+    $ottoDir/current/
+ln -sf $ottoDir/current/nextstrain{Discarded,Blacklisted,Informative}.bb \
+    $ottoDir/current/nextstrainParsimony.bw \
     $gbdbDir/
 
-# Archive
+# Daily archive (may overwrite files from earlier today)
 mkdir -p $ottoDir/archive/$today
 cp -pf $runDir/nextstrainGene.bb $runDir/nextstrainClade.bb \
     $runDir/nextstrain*.vcf.gz{,.tbi} \
     $runDir/nextstrain*.nh \
     $runDir/ncov.json \
     $ottoDir/archive/$today
 
 echo "Updated nextstrain/ncov `date` (ncov.json date $latestDate)"