db96d28dd92f6ad538d7f07ef1ee600bbd599fa7
angie
  Tue May 12 09:47:32 2020 -0700
Use more force when downloading latest ncov.json so the script doesn't die if there's a read-only ncov.json file in the way.  refs #25188

diff --git src/hg/utils/otto/nextstrainNcov/doUpdate.sh src/hg/utils/otto/nextstrainNcov/doUpdate.sh
index 8492ccd..2ba399e 100755
--- src/hg/utils/otto/nextstrainNcov/doUpdate.sh
+++ src/hg/utils/otto/nextstrainNcov/doUpdate.sh
@@ -1,46 +1,47 @@
 #!/bin/bash
 set -beEu -o pipefail
 
 #	Do not modify this script, modify the source tree copy:
 #	kent/src/hg/utils/nextstrainNcov/doUpdate.sh
 
 ottoDir=/hive/data/outside/otto/nextstrainNcov
 chromSizes=/hive/data/genomes/wuhCor1/chrom.sizes
 gbdbDir=/gbdb/wuhCor1/nextstrain
 
 ncovJsonUrl='https://nextstrain.org/charon/getDataset?prefix=/ncov/global'
 
 cd $ottoDir
 
 # The file is named .json, but is actually gzipped, so gunzip it.
+rm -f ncov.json
 curl -s "$ncovJsonUrl" \
 | gunzip -c > ncov.json
 curl -s -I "$ncovJsonUrl" \
 | grep Last-Mod | sed -re 's/Last-Modified: //; s/\r//;' \
    > ncov.json.date
 latestDate=$(cat ncov.json.date)
 oldDate=$(cat old.ncov.json.date)
 if [ $(date -d "$latestDate" +%s) -le $(date -d "$oldDate" +%s)  ]; then
     exit 0
 fi
 
 today=`date +%F`
 mkdir -p $today
 ncovTime=$(date -d "$latestDate" +%F-%H:%M)
 cp -p ncov.json $today/ncov.$ncovTime.json
-mv ncov.json old.ncov.json
+mv -f ncov.json old.ncov.json
 mv ncov.json.date old.ncov.json.date
 
 runDir=$ottoDir/$today
 cd $runDir
 chmod 444 ncov.$ncovTime.json
 ln -sf ncov.$ncovTime.json ncov.json
 
 #Generate bed and VCF files
 $ottoDir/nextstrain.py
 
 # bgzip & tabix the VCF files
 bgzip -f nextstrainSamples.vcf
 tabix -p vcf nextstrainSamples.vcf.gz
 for clade in A1a A2 A2a A3 A6 A7 B B1 B2 B4; do
   bgzip -f nextstrainSamples$clade.vcf