3a74edab38d1a6e928729bc6b4feec3762ee2f40
angie
  Tue Nov 14 17:05:26 2023 -0800
Don't offer uncompressed protobuf for download (only compressed). Also don't offer redundant .nextclade.pangolin version of same file.

diff --git src/hg/utils/otto/sarscov2phylo/extractPublicTree.sh src/hg/utils/otto/sarscov2phylo/extractPublicTree.sh
index 3e5f83a..6ebf17f 100755
--- src/hg/utils/otto/sarscov2phylo/extractPublicTree.sh
+++ src/hg/utils/otto/sarscov2phylo/extractPublicTree.sh
@@ -104,44 +104,41 @@
     --clade_types=nextstrain,pango \
     --name_internal_nodes \
     --title "$today tree with sequences from GISAID, INSDC, COG-UK and CNCB" \
     --output public-$today.all.masked.taxonium.jsonl.gz >& utt.log
 
 # Make a size-limited public tree for ShUShER so it doesn't exceed browser memory limits
 $matUtils extract -i public-$today.all.masked.pb --set-size 6000000 \
     -o public-$today.all.masked.ShUShER.pb.gz
 
 # Link to public trees download directory hierarchy
 archiveRoot=/hive/users/angie/publicTrees
 read y m d < <(echo $today | sed -re 's/-/ /g')
 archive=$archiveRoot/$y/$m/$d
 mkdir -p $archive
 gzip -c public-$today.all.nwk > $archive/public-$today.all.nwk.gz
-ln -f `pwd`/public-$today.all.masked.{pb,vcf.gz} $archive/
+ln -f `pwd`/public-$today.all.masked.vcf.gz $archive/
 gzip -c public-$today.all.masked.pb > $archive/public-$today.all.masked.pb.gz
 ln -f `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 lineageToPublicName > $archive/lineageToPublicName.tsv.gz
 gzip -c cladeToPublicName > $archive/cladeToPublicName.tsv.gz
 ln -f `pwd`/hgPhyloPlace.description.txt $archive/public-$today.version.txt
 ln -f `pwd`/public-$today.all.masked.taxonium.jsonl.gz $archive/
 ln -f `pwd`/public-$today.all.masked.ShUShER.pb.gz $archive/
 
 # Update 'latest' in $archiveRoot
 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
 ln -f $archive/public-$today.all.masked.taxonium.jsonl.gz \
     $archiveRoot/public-latest.all.masked.taxonium.jsonl.gz
 ln -f $archive/public-$today.all.masked.ShUShER.pb.gz \
     $archiveRoot/public-latest.all.masked.ShUShER.pb.gz
 
 # Update hgdownload-test link for archive
 mkdir -p /usr/local/apache/htdocs-hgdownload/goldenPath/wuhCor1/UShER_SARS-CoV-2/$y/$m
 ln -sf $archive /usr/local/apache/htdocs-hgdownload/goldenPath/wuhCor1/UShER_SARS-CoV-2/$y/$m
 
 # Update links to latest public protobuf and metadata in hgwdev cgi-bin directories
 pigz -p 8 -c samples.public.$today > samples.public.$today.gz