60cefbcaddbd1627848c16242aa8145a5186e6a4
angie
  Thu Aug 19 20:28:13 2021 -0700
Use matUtils extract's new option to write protobuf for the awesome Taxodium viewer (cov2tree.org); add it to public downloads.

diff --git src/hg/utils/otto/sarscov2phylo/updateCombinedTree.sh src/hg/utils/otto/sarscov2phylo/updateCombinedTree.sh
index 2d900ab..a2d68e2 100755
--- src/hg/utils/otto/sarscov2phylo/updateCombinedTree.sh
+++ src/hg/utils/otto/sarscov2phylo/updateCombinedTree.sh
@@ -450,16 +450,27 @@
 | sort > lineageToName
 
 # EPI_ISL_ ID to public sequence name mapping, so if users upload EPI_ISL IDs for which we have
 # public names & IDs, we can match them.
 cut -f 1,3 $epiToPublic > epiToPublic.latest
 
 # Update links to latest public+GISAID protobuf and metadata in hgwdev cgi-bin directories
 for dir in /usr/local/apache/cgi-bin{-angie,-beta,}/hgPhyloPlaceData/wuhCor1; do
     ln -sf `pwd`/gisaidAndPublic.$today.masked.pb $dir/public.plusGisaid.latest.masked.pb
     ln -sf `pwd`/gisaidAndPublic.$today.metadata.tsv.gz \
         $dir/public.plusGisaid.latest.metadata.tsv.gz
     ln -sf `pwd`/hgPhyloPlace.plusGisaid.description.txt $dir/public.plusGisaid.latest.version.txt
     ln -sf `pwd`/epiToPublic.latest $dir/
 done
 
+# Make Taxodium-formatted protobuf for display
+zcat /hive/data/genomes/wuhCor1/goldenPath/bigZips/genes/ncbiGenes.gtf.gz > ncbiGenes.gtf
+zcat gisaidAndPublic.$today.metadata.tsv.gz > metadata.tmp.tsv
+time $matUtils extract -i gisaidAndPublic.$today.masked.pb \
+    -f reference.fa \
+    -g ncbiGenes.gtf \
+    -M metadata.tmp.tsv \
+    --write-taxodium gisaidAndPublic.$today.masked.taxodium.pb
+rm metadata.tmp.tsv
+gzip gisaidAndPublic.$today.masked.taxodium.pb
+
 $scriptDir/extractPublicTree.sh $today