6aa3eabbd7f14c3f3260183f0cbbf54e2c176724
angie
  Mon Apr 19 15:41:28 2021 -0700
Oops, fix some paths & typos for gzipping public tree archive files.

diff --git src/hg/utils/otto/sarscov2phylo/updatePublicTree.sh src/hg/utils/otto/sarscov2phylo/updatePublicTree.sh
index 585eb51..20006c6 100755
--- src/hg/utils/otto/sarscov2phylo/updatePublicTree.sh
+++ src/hg/utils/otto/sarscov2phylo/updatePublicTree.sh
@@ -390,34 +390,34 @@
             /gbdb/wuhCor1/sarsCov2PhyloPub/public.$q.minAf.$af.vcf.gz
     done
 done
 fi
 
 # Link to public trees download directory hierarchy
 archiveRoot=/hive/users/angie/publicTrees
 archive=$archiveRoot/$y/$m/$d
 mkdir -p $archive
 gzip -c public-$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 $archive/
 gzip -c public-$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
+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 $y/$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
+ln -f $archive/public-$today.all.nwk.gz $archiveRoot/public-latest.all.nwk.gz
+ln -f $archive/public-$today.all.masked.pb $archiveRoot/public-latest.all.masked.pb
+ln -f $archive/public-$today.all.masked.pb.gz $archiveRoot/public-latest.all.masked.pb.gz
+ln -f $archive/public-$today.all.masked.vcf.gz $archiveRoot/public-latest.all.masked.vcf.gz
+ln -f $archive/public-$today.metadata.tsv.gz $archiveRoot/public-latest.metadata.tsv.gz
+ln -f $archive/public-$today.version.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