655174351c1c50009ea8e8af21ad0b15d8231e55
angie
  Tue Apr 13 23:15:03 2021 -0700
gzip-compress the public tree download files.  Leave around an uncompressed copy of public-*.masked.pb in case somebody's script depends on it.

diff --git src/hg/utils/otto/sarscov2phylo/updatePublicTree.sh src/hg/utils/otto/sarscov2phylo/updatePublicTree.sh
index 1a5b826..585eb51 100755
--- src/hg/utils/otto/sarscov2phylo/updatePublicTree.sh
+++ src/hg/utils/otto/sarscov2phylo/updatePublicTree.sh
@@ -1,419 +1,423 @@
 #!/bin/bash
 set -beEu -x -o pipefail
 
 #	Do not modify this script, modify the source tree copy:
 #	kent/src/hg/utils/otto/sarscov2phylo/updatePublicTree.sh
 
 usage() {
     echo "usage: $0 prevDate problematicSitesVcf"
     echo "This assumes that ncbi.latest and cogUk.latest links/directories have been updated."
 }
 
 if [ $# != 2 ]; then
   usage
   exit 1
 fi
 
 ottoDir=/hive/data/outside/otto/sarscov2phylo
 prevDate=$1
 problematicSitesVcf=$2
 prevVcf=$ottoDir/$prevDate/public-$prevDate.all.vcf.gz
 prevProtobufMasked=$ottoDir/$prevDate/public-$prevDate.all.masked.pb
 prevProtobufUnmasked=$ottoDir/$prevDate/public-$prevDate.all.notMasked.pb
 prevMeta=$ottoDir/$prevDate/public-$prevDate.metadata.tsv.gz
 
 echo "prevVcf=$prevVcf"
 echo "prevProtobufMasked=$prevProtobufMasked"
 echo "prevProtobufUnmasked=$prevProtobufUnmasked"
 echo "prevMeta=$prevMeta"
 echo "problematicSitesVcf=$problematicSitesVcf"
 
 ncbiDir=$ottoDir/ncbi.latest
 cogUkDir=$ottoDir/cogUk.latest
 cncbDir=$ottoDir/cncb.latest
 today=$(date +%F)
+y=$(date +%Y)
+m=$(date +%m)
+d=$(date +%d)
 
 minReal=20000
 ref2bit=/hive/data/genomes/wuhCor1/wuhCor1.2bit
 
 usherDir=~angie/github/usher
 usher=$usherDir/build/usher
 matUtils=$usherDir/build/matUtils
 find_parsimonious_assignments=~angie/github/strain_phylogenetics/build/find_parsimonious_assignments
 
 scriptDir=$(dirname "${BASH_SOURCE[0]}")
 
 source $scriptDir/util.sh
 
 # Before we get started, make sure cog_metadata has the columns we're expecting:
 expectedHeaderStart='sequence_name,country,adm1,pillar_2,sample_date,epi_week,lineage,'
 cogUkMetHeader=$(head -1 $cogUkDir/cog_metadata.csv | grep ^$expectedHeaderStart)
 # The grep will fail if they change one of the first 7 fields.
 # If it fails, update cog_metadata.csv column indices below and in getCogUk.sh too.
 
 mkdir -p $ottoDir/$today
 cd $ottoDir/$today
 
 # Disregard pipefail just for this pipe because head prevents the cat from completing:
 set +o pipefail
 xcat $prevVcf | head | grep ^#CHROM | sed -re 's/\t/\n/g;' | tail -n+10 > prevNames
 set -o pipefail
 awk -F\| '{if ($3 == "") { print $1; } else { print $2; } }' prevNames \
 | grep -E '^[A-Z]{2}[0-9]{6}\.[0-9]' > prevGbAcc
 awk -F\| '{if ($3 == "") { print $1; } else { print $2; } }' prevNames \
 | grep -E '^(England|Northern|Scotland|Wales)' > prevCogUk
 
 # Get new GenBank sequences with at least $minReal non-N bases.
 xzcat $ncbiDir/genbank.fa.xz \
 | faSomeRecords -exclude stdin prevGbAcc newGenBank.fa
 faSize -veryDetailed newGenBank.fa \
 | tawk '$4 < '$minReal' {print $1;}' \
     > gbTooSmall
 # NCBI also includes NC_045512 in the download, but that's our reference, so... exclude that too.
 fastaNames newGenBank.fa | grep NC_045512 >> gbTooSmall
 faSomeRecords -exclude newGenBank.fa gbTooSmall newGenBank.filtered.fa
 faSize newGenBank.filtered.fa
 
 # Get new COG-UK sequences with at least $minReal non-N bases.
 xzcat $cogUkDir/cog_all.fasta.xz \
 | faSomeRecords -exclude stdin prevCogUk newCogUk.fa
 faSize -veryDetailed newCogUk.fa \
 | tawk '$4 < '$minReal' {print $1;}' \
     > cogUkTooSmall
 faSomeRecords -exclude newCogUk.fa cogUkTooSmall newCogUk.filtered.fa
 faSize newCogUk.filtered.fa
 
 cat newGenBank.filtered.fa newCogUk.filtered.fa > new.fa
 
 # Some days there are no new public sequences; just link to yesterday's results.
 # Temporarily disable pipefail because fastaNames uses grep which fails when there are no sequences.
 set +o pipefail
 newSeqCount=$(fastaNames new.fa | wc -l)
 set -o pipefail
 if [ $newSeqCount == 0 ] ; then
     ln -sf $prevVcf public-$today.all.vcf.gz
     ln -sf $prevProtobufMasked public-$today.all.masked.pb
     ln -sf $prevProtobufUnmasked public-$today.all.notMasked.pb
     ln -sf $prevMeta public-$today.metadata.tsv.gz
     echo "No new sequences; linking to yesterday's results."
     exit 0
 fi
 
 # Use Rob's script that aligns each sequence to NC_045512.2 and concatenates the results
 # as a multifasta alignment (from which we can extract VCF with SNVs):
 #conda install -c bioconda mafft
 alignedFa=new.aligned.fa
 rm -f $alignedFa
 export TMPDIR=/dev/shm
 time bash ~angie/github/sarscov2phylo/scripts/global_profile_alignment.sh \
   -i new.fa \
   -o $alignedFa \
   -t 50
 faSize $alignedFa
 
 # Now make a renaming that keeps all the prevNames and adds full names (with shortened dates)
 # for the new seqs.
 renaming=oldAndNewNames
 tawk '{print $1, $1;}' prevNames > $renaming
 if (( $(fastaNames newCogUk.filtered.fa | wc -l) > 0 )) ; then
     # This grep failed 2021-03-14, crashing the script.  I complained to COG-UK; tolerate.
     set +o pipefail
     fastaNames newCogUk.filtered.fa \
     | grep -Fwf - $cogUkDir/cog_metadata.csv \
     | awk -F, '{print $1 "\t" $1 "|" $5;}' \
     | sed -re 's/20([0-9][0-9])(-[0-9-]+)?$/\1\2/;' \
         >> $renaming
     set -o pipefail
 fi
 if (( $(fastaNames newGenBank.filtered.fa | wc -l) > 0 )) ; then
     fastaNames newGenBank.filtered.fa \
     | sed -re 's/[ |].*//' \
     | grep -Fwf - $ncbiDir/ncbi_dataset.plusBioSample.tsv \
     | tawk '{ if ($3 == "") { $3 = "?"; }
               if ($6 != "") { print $1 "\t" $6 "|" $1 "|" $3; }
               else { print $1 "\t" $1 "|" $3; } }' \
     | cleanGenbank \
     | sed -re 's/ /_/g' \
     | sed -re 's/20([0-9][0-9])(-[0-9-]+)?$/\1\2/;' \
         >> $renaming
 fi
 wc -l $renaming
 
 # Make VCF -- first without masking, for hgTracks
 time cat <(twoBitToFa $ref2bit stdout) $alignedFa \
 | faToVcf stdin stdout \
 | vcfRenameAndPrune stdin $renaming stdout \
 | gzip -c \
     > new.vcf.gz
 # Use usher to add new public sequences to tree of mapped subset and infer missing/ambig bases.
 time $usher -u -T 50 \
     -v new.vcf.gz \
     -i $prevProtobufUnmasked \
     -o public-$today.all.notMasked.pb \
     >& usher.addNewUnmasked.log
 #~10 hours for 56k seqs, ~72m for 6k
 $matUtils extract -i public-$today.all.notMasked.pb -v public-$today.all.vcf
 ls -l public-$today.all.vcf
 wc -l public-$today.all.vcf
 bgzip -f public-$today.all.vcf
 tabix -p vcf public-$today.all.vcf.gz
 
 # Then with masking to collapse the tree & make protobuf for usher/hgPhyloPlace:
 tawk '{ if ($1 ~ /^#/) { print; } else if ($7 == "mask") { $1 = "NC_045512v2"; print; } }' \
     $problematicSitesVcf > mask.vcf
 time vcfFilter -excludeVcf=mask.vcf new.vcf.gz \
 | gzip -c \
     > new.masked.vcf.gz
 time $usher -u -T 50 \
     -v new.masked.vcf.gz \
     -i $prevProtobufMasked \
     -o public-$today.all.masked.pb \
     >& usher.addNew.log
 mv uncondensed-final-tree.nh public-$today.all.nwk
 # Masked VCF that goes with the masked protobuf, for public distribution for folks who want
 # to run UShER and also have the VCF.
 $matUtils extract -i public-$today.all.masked.pb -v public-$today.all.masked.vcf
 gzip public-$today.all.masked.vcf
 
 # Make allele-frequency-filtered versions
 # Disregard pipefail just for this pipe because head prevents the cat from completing:
 set +o pipefail
 sampleCount=$(zcat public-$today.all.vcf.gz | head | grep ^#CHROM | sed -re 's/\t/\n/g' \
               | tail -n+10 | wc -l)
 set -o pipefail
 minAc001=$(( (($sampleCount + 999) / 1000) ))
 vcfFilter -minAc=$minAc001 -rename public-$today.all.vcf.gz \
     > public-$today.all.minAf.001.vcf
 wc -l public-$today.all.minAf.001.vcf
 bgzip -f public-$today.all.minAf.001.vcf
 tabix -p vcf public-$today.all.minAf.001.vcf.gz
 
 minAc01=$(( (($sampleCount + 99) / 100) ))
 vcfFilter -minAc=$minAc01 -rename public-$today.all.minAf.001.vcf.gz \
     > public-$today.all.minAf.01.vcf
 wc -l public-$today.all.minAf.01.vcf
 bgzip -f public-$today.all.minAf.01.vcf
 tabix -p vcf public-$today.all.minAf.01.vcf.gz
 
 # Parsimony scores on collapsed tree
 time $find_parsimonious_assignments --tree public-$today.all.nwk \
     --vcf <(gunzip -c public-$today.all.vcf.gz) \
 | tail -n+2 \
 | sed -re 's/^[A-Z]([0-9]+)[A-Z,]+.*parsimony_score=([0-9]+).*/\1\t\2/;' \
 | tawk '{print "NC_045512v2", $1-1, $1, $2;}' \
 | sort -k2n,2n \
     > public-$today.all.parsimony.bg
 bedGraphToBigWig public-$today.all.parsimony.bg /hive/data/genomes/wuhCor1/chrom.sizes \
     public-$today.all.parsimony.bw
 
 # Metadata for hgPhyloPlace:
 # Header names same as nextmeta (with strain first) so hgPhyloPlace recognizes them:
 echo -e "strain\tgenbank_accession\tdate\tcountry\thost\tcompleteness\tlength\tNextstrain_clade\tpangolin_lineage" \
     > public-$today.metadata.tsv
 # It's not always possible to recreate both old and new names correctly from metadata,
 # so make a file to translate accession or COG-UK to the name used in VCF, tree and protobufs.
 cut -f 2 $renaming \
 | awk -F\| '{ if ($3 == "") { print $1 "\t" $0; } else { print $2 "\t" $0; } }' \
 | sort \
     > idToName
 # NCBI metadata (strip colon-separated location after country if present):
 tawk '$8 >= 20000 { print $1, $3, $4, $5, $6, $8; }' \
     $ncbiDir/ncbi_dataset.plusBioSample.tsv \
 | sed -re 's/\t([A-Za-z -]+):[A-Za-z0-9 ,()_-]+\t/\t\1\t/;' \
 | perl -wpe '@w = split("\t"); $w[4] =~ s/ /_/g; $_ = join("\t", @w);' \
 | cleanGenbank \
 | sort > gb.metadata
 if [ -e $ncbiDir/lineage_report.csv ]; then
     echo Getting GenBank Pangolin lineages from $ncbiDir/lineage_report.csv
     tail -n+2  $ncbiDir/lineage_report.csv \
     | sed -re 's/^([A-Z][A-Z][0-9]{6}\.[0-9]+)[^,]*/\1/;' \
     | awk -F, '$2 != "" && $2 != "None" {print $1 "\t" $2;}' \
     | sort \
         > gbToLineage
 else
     echo Getting GenBank Pangolin lineages from $prevMeta
     zcat $prevMeta \
     | tail -n+2 \
     | tawk '$2 != "" && $8 != "" { print $2, $8; }' \
     | sort \
         > gbToLineage
 fi
 wc -l gbToLineage
 if [ -e $ncbiDir/nextclade.tsv ]; then
     sort $ncbiDir/nextclade.tsv > gbToNextclade
 else
     touch gbToNextclade
 fi
 wc -l gbToNextclade
 join -t$'\t' -a 1 gb.metadata gbToNextclade \
 | join -t$'\t' -a 1 - gbToLineage \
 | tawk '{ if ($2 == "") { $2 = "?"; }
           print $1, $1, $2, $3, $4, "", $6, $7, $8; }' \
 | join -t$'\t' -o 1.2,2.2,2.3,2.4,2.5,2.6,2.7,2.8,2.9 idToName - \
     >> public-$today.metadata.tsv
 # COG-UK metadata:
 if [ -e $cogUkDir/nextclade.tsv ]; then
     sort $cogUkDir/nextclade.tsv > cogUkToNextclade
 else
     touch cogUkToNextclade
 fi
 #*** Could also add sequence length to metadata from faSizes output...
 tail -n+2 $cogUkDir/cog_metadata.csv \
 | awk -F, -v 'OFS=\t' '{print $1, "", $5, $2, "", "", "", $7; }' \
 | sort \
 | join -t$'\t' -a 1 -o 1.1,1.2,1.3,1.4,1.5,1.6,1.7,2.2,1.8 - cogUkToNextclade \
 | join -t$'\t' -o 1.2,2.2,2.3,2.4,2.5,2.6,2.7,2.8,2.9 idToName - \
     >> public-$today.metadata.tsv
 # CNCB metadata:
 tail -n+2 $cncbDir/cncb.metadata.tsv \
 | tawk '{ if ($3 != "GISAID" && $3 != "GenBank" && $3 != "Genbank") {
             print $2, "", $10, $11, $9, $5, $6} }' \
 | sed -re 's@\t([A-Za-z -]+)( / [A-Za-z -'"'"']+)+\t@\t\1\t@;  s/Sapiens/sapiens/;' \
 | sort \
 | join -t$'\t' -a 1 -o 1.1,1.2,1.3,1.4,1.5,1.6,1.7,2.2 - $cncbDir/nextclade.tsv \
 | join -t$'\t' -a 1 -o 1.1,1.2,1.3,1.4,1.5,1.6,1.7,1.8,2.2 - $cncbDir/pangolin.tsv \
 | join -t$'\t' -o 1.2,2.2,2.3,2.4,2.5,2.6,2.7,2.8,2.9 idToName - \
     >> public-$today.metadata.tsv
 wc -l public-$today.metadata.tsv
 gzip -f public-$today.metadata.tsv
 
 # Lineage colors:
 zcat public-$today.metadata.tsv.gz \
 | tail -n+2 \
 | tawk '$8 != "" || $9 != "" { print $1, $8, $9, ""; }' \
 | sort -u > sampleToLineage
 wc -l sampleToLineage
 ~/kent/src/hg/utils/otto/sarscov2phylo/cladeLineageColors.pl sampleToLineage
 rm gisaidColors
 mv lineageColors public-$today.lineageColors
 mv nextstrainColors public-$today.nextstrainColors
 gzip -f public-$today.lineageColors public-$today.nextstrainColors
 
 #***TODO: make acknowledgements.tsv.gz! (see publicCredits.sh)
 
 ncbiDate=$(ls -l $ncbiDir | sed -re 's/.*ncbi\.([0-9]{4}-[0-9][0-9]-[0-9][0-9]).*/\1/')
 cogUkDate=$(ls -l $cogUkDir | sed -re 's/.*cogUk\.([0-9]{4}-[0-9][0-9]-[0-9][0-9]).*/\1/')
 cncbDate=$(ls -l $cncbDir | sed -re 's/.*cncb\.([0-9]{4}-[0-9][0-9]-[0-9][0-9]).*/\1/')
 if [ $ncbiDate == $cogUkDate ]; then
     echo "sarscov2phylo release 13-11-20; NCBI and COG-UK sequences downloaded $ncbiDate; CNCB sequences downloaded $cncbDate" \
         > version.txt
 else
     echo "sarscov2phylo release 13-11-20; NCBI sequences downloaded $ncbiDate; COG-UK sequences downloaded $cogUkDate; CNCB sequences downloaded $cncbDate" \
         > version.txt
 fi
 
 sampleCountComma=$(echo $sampleCount \
                    | sed -re 's/([0-9]+)([0-9]{3})$/\1,\2/; s/([0-9]+)([0-9]{3},[0-9]{3})$/\1,\2/;')
 echo "$sampleCountComma genomes from GenBank, COG-UK and CNCB ($today); sarscov2phylo 13-11-20 tree with newer sequences added by UShER" \
     > hgPhyloPlace.description.txt
 
 cp -p public-$today.all.masked.pb{,.bak}
 
 # Add nextclade annotations to protobuf
 zcat public-$today.metadata.tsv.gz \
 | tail -n+2 | tawk '$8 != "" {print $8, $1;}' \
 | sed -re 's/^20E \(EU1\)/20E.EU1/;' \
     > cladeToPublicName
 time $matUtils annotate -T 50 \
     -l \
     -i public-$today.all.masked.pb \
     -c cladeToPublicName \
     -o public-$today.all.masked.nextclade.pb \
     >& annotate.nextclade.out
 
 # Add pangolin lineage annotations to protobuf
 zcat public-$today.metadata.tsv.gz \
 | tail -n+2 | tawk '$9 != "" {print $9, $1;}' \
     > lineageToPublicName
 time $matUtils annotate -T 50 \
     -i public-$today.all.masked.nextclade.pb \
     -c lineageToPublicName \
     -o public-$today.all.masked.nextclade.pangolin.pb \
     >& annotate.pangolin.out
 
 # Not all the Pangolin lineages can be assigned nodes so for now just use nextclade
 cp -p public-$today.all.masked.nextclade.pb public-$today.all.masked.pb
 
 # Divide up allele-frequency-filtered versions into quarterly versions
 set +o pipefail
 zcat public-$today.all.vcf.gz | head | grep ^#CHROM | sed -re 's/\t/\n/g' | tail -n+10 \
 | awk -F\| '{if ($3 == "") { print $2 "\t" $0; } else { print $3 "\t" $0;} }' \
 | egrep '^[0-9][0-9]-[0-9][0-9]' \
 | sed -re 's/^([0-9][0-9])-([0-9][0-9])(-[0-9][0-9])?(.*)/\1\t\2\4/;' \
 | tawk '($1 == 19 && $2 == 12) || ($1 > 19 && $2 > 0)' \
 | sort > samplesByDate
 set -o pipefail
 
 tawk '$1 < 20 || ($1 == 20 && $2 <= 3) { print $3, $3; }' samplesByDate \
     > 20Q1.renaming
 tawk '$1 == 20 && $2 >= 4 && $2 <= 6 { print $3, $3; }' samplesByDate \
     > 20Q2.renaming
 tawk '$1 == 20 && $2 >= 7 && $2 <= 9 { print $3, $3; }' samplesByDate \
     > 20Q3.renaming
 tawk '$1 == 20 && $2 >= 10 { print $3, $3; }' samplesByDate \
     > 20Q4.renaming
 tawk '$1 == 21 && $2 <= 3{ print $3, $3; }' samplesByDate \
     > 21Q1.renaming
 
 for q in 20Q1 20Q2 20Q3 20Q4 21Q1; do
     for af in 01 001; do
         vcfRenameAndPrune public-$today.all.minAf.$af.vcf.gz $q.renaming \
             public-$today.$q.minAf.$af.vcf
         wc -l public-$today.$q.minAf.$af.vcf
         bgzip public-$today.$q.minAf.$af.vcf
         tabix -p vcf public-$today.$q.minAf.$af.vcf.gz
     done
 done
 
 # Update gbdb links -- not every day, too much churn for getting releases out and the
 # tracks are getting unmanageably large for VCF.
 if false; then
 for f in public-$today.all{,.minAf*}.vcf.gz ; do
     t=$(echo $f | sed -re "s/-$today//;")
     ln -sf `pwd`/$f /gbdb/wuhCor1/sarsCov2PhyloPub/$t
     ln -sf `pwd`/$f.tbi /gbdb/wuhCor1/sarsCov2PhyloPub/$t.tbi
 done
 ln -sf `pwd`/public-$today.all.nwk /gbdb/wuhCor1/sarsCov2PhyloPub/public.all.nwk
 ln -sf `pwd`/public-$today.all.parsimony.bw \
     /gbdb/wuhCor1/sarsCov2PhyloPub/public.all.parsimony.bw
 ln -sf `pwd`/public-$today.lineageColors.gz \
     /gbdb/wuhCor1/sarsCov2PhyloPub/public.all.lineageColors.gz
 ln -sf `pwd`/public-$today.nextstrainColors.gz \
     /gbdb/wuhCor1/sarsCov2PhyloPub/public.all.nextstrainColors.gz
 ln -sf `pwd`/version.txt /gbdb/wuhCor1/sarsCov2PhyloPub/public.all.version.txt
 for q in 20Q1 20Q2 20Q3 20Q4 21Q1; do
     for af in 01 001; do
         ln -sf `pwd`/public-$today.$q.minAf.$af.vcf.gz \
             /gbdb/wuhCor1/sarsCov2PhyloPub/public.$q.minAf.$af.vcf.gz
     done
 done
 fi
 
 # Link to public trees download directory hierarchy
-y=$(date +%Y)
-m=$(date +%m)
-d=$(date +%d)
 archiveRoot=/hive/users/angie/publicTrees
 archive=$archiveRoot/$y/$m/$d
 mkdir -p $archive
-ln `pwd`/public-$today.all.nwk $archive/
+gzip -c public-$today.all.nwk > $archive/public-$today.all.nwk.gz
 ln `pwd`/public-$today.all.masked.{pb,vcf.gz} $archive/
+gzip -c public-$today.all.masked.pb > $archive/public-$today.all.masked.pb.gz
 ln `pwd`/public-$today.metadata.tsv.gz $archive/
-ln `pwd`/public-$today.all.masked.nextclade.pangolin.pb $archive/
-ln `pwd`/cladeToPublicName $archive/
-ln `pwd`/lineageToPublicName $archive/
+gzip -c public-$today.all.masked.nextclade.pangolin.pb \
+    > $archive/public-$today.all.masked.nextclade.pangolin.pb.gz
+gzip -c cladeToPublicName $archive/cladeToPublicName.gz
+gzip -c lineageToPublicName $archive/lineageToPublicName.gz
+ln `pwd`/hgPhyloPlace.description.txt $archive/public-$today.version.txt
 
 # Update 'latest' in $archiveRoot
-ln -f `pwd`/public-$today.all.nwk $archiveRoot/public-latest.all.nwk
-ln -f `pwd`/public-$today.all.masked.pb $archiveRoot/public-latest.all.masked.pb
-ln -f `pwd`/public-$today.all.masked.vcf.gz $archiveRoot/public-latest.all.masked.vcf.gz
-ln -f `pwd`/public-$today.metadata.tsv.gz $archiveRoot/public-latest.metadata.tsv.gz
-ln -f `pwd`/hgPhyloPlace.description.txt $archiveRoot/public-latest.version.txt
+ln -f $y/$m/$d/public-$today.all.nwk.gz $archiveRoot/public-latest.all.nwk.gz
+ln -f $y/$m/$d/public-$today.all.masked.pb $archiveRoot/public-latest.all.masked.pb
+ln -f $y/$m/$d/public-$today.all.masked.pb.gz $archiveRoot/public-latest.all.masked.pb.gz
+ln -f $y/$m/$d/public-$today.all.masked.vcf.gz $archiveRoot/public-latest.all.masked.vcf.gz
+ln -f $y/$m/$d/public-$today.metadata.tsv.gz $archiveRoot/public-latest.metadata.tsv.gz
+ln -f $y/$m/$d/hgPhyloPlace.description.txt $archiveRoot/public-latest.version.txt
 
 # Update 'latest' protobuf, metadata and desc in and cgi-bin{,-angie}/hgPhyloPlaceData/wuhCor1/
 for dir in /usr/local/apache/cgi-bin{-angie,-beta,}/hgPhyloPlaceData/wuhCor1; do
     ln -sf `pwd`/public-$today.all.masked.pb $dir/public-latest.all.masked.pb
     ln -sf `pwd`/public-$today.metadata.tsv.gz $dir/public-latest.metadata.tsv.gz
     ln -sf `pwd`/hgPhyloPlace.description.txt $dir/public-latest.version.txt
 done