03c00c97bfb4666cbc74b63bf06a62948ff643ee
angie
  Sun Apr 19 14:36:54 2020 -0700
Add -f now that I'm write-protecting the timestamped ncov.json copies.  refs #25188

diff --git src/hg/utils/otto/nextstrainNcov/doUpdate.sh src/hg/utils/otto/nextstrainNcov/doUpdate.sh
index 8f25ca2..06d02bd 100755
--- src/hg/utils/otto/nextstrainNcov/doUpdate.sh
+++ src/hg/utils/otto/nextstrainNcov/doUpdate.sh
@@ -46,28 +46,28 @@
   bgzip -f nextstrainSamples$clade.vcf
   tabix -p vcf nextstrainSamples$clade.vcf.gz
 done
 
 # bigBed-ify the gene names and "clades"
 bedToBigBed -type=bed4 -tab -verbose=0 nextstrainGene.bed $chromSizes \
     nextstrainGene.bb
 
 sort -k2n,2n nextstrainClade.bed > nextstrainClade.sorted.bed
 bedToBigBed -as=$ottoDir/nextstrainClade.as -type=bed12+7 -tab -verbose=0 \
     nextstrainClade.sorted.bed $chromSizes \
     nextstrainClade.bb
 
 # Archive
 mkdir -p $ottoDir/archive/$today
-cp -p $runDir/nextstrainGene.bb $runDir/nextstrainClade.bb \
+cp -pf $runDir/nextstrainGene.bb $runDir/nextstrainClade.bb \
     $runDir/nextstrainSamples*.vcf.gz{,.tbi} \
     $runDir/nextstrain*.nh \
     $runDir/ncov.json \
     $ottoDir/archive/$today
 
 # Install
 ln -sf $runDir/nextstrainGene.bb $runDir/nextstrainClade.bb \
     $runDir/nextstrainSamples*.vcf.gz{,.tbi} \
     $runDir/nextstrain*.nh \
     $gbdbDir/
 
 echo "Updated nextstrain/ncov `date` (ncov.json date $latestDate)"