abdea7a81b3d511adaee6300277721a804f5581f
angie
  Tue Mar 30 11:57:47 2021 -0700
Ongoing fixes for odd characters in sequence names and other pipeline tweaks.

diff --git src/hg/utils/otto/sarscov2phylo/updatePublicTree.sh src/hg/utils/otto/sarscov2phylo/updatePublicTree.sh
index 8a750ff..1a5b826 100755
--- src/hg/utils/otto/sarscov2phylo/updatePublicTree.sh
+++ src/hg/utils/otto/sarscov2phylo/updatePublicTree.sh
@@ -399,23 +399,21 @@
 ln `pwd`/public-$today.all.nwk $archive/
 ln `pwd`/public-$today.all.masked.{pb,vcf.gz} $archive/
 ln `pwd`/public-$today.metadata.tsv.gz $archive/
 ln `pwd`/public-$today.all.masked.nextclade.pangolin.pb $archive/
 ln `pwd`/cladeToPublicName $archive/
 ln `pwd`/lineageToPublicName $archive/
 
 # 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
 
 # Update 'latest' protobuf, metadata and desc in and cgi-bin{,-angie}/hgPhyloPlaceData/wuhCor1/
-for dir in /usr/local/apache/cgi-bin{-angie,-demo-angie,-beta,}/hgPhyloPlaceData/wuhCor1; do
+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
 
-# Clean up
-nice xz new*fa &