c8d7abe94b3244702501b71b62d9e1ea6333228b
angie
  Sat Jan 23 14:24:20 2021 -0800
Grab COG-UK daily tree as Russ suggests; might want to try using it instead of GISAID tree.

diff --git src/hg/utils/otto/sarscov2phylo/getCogUk.sh src/hg/utils/otto/sarscov2phylo/getCogUk.sh
index b2affda..f17146f 100755
--- src/hg/utils/otto/sarscov2phylo/getCogUk.sh
+++ src/hg/utils/otto/sarscov2phylo/getCogUk.sh
@@ -5,21 +5,22 @@
 # Download latest COG-UK fasta and metadata; update $ottoDir/cogUk.latest link.
 
 scriptDir=$(dirname "${BASH_SOURCE[0]}")
 source $scriptDir/util.sh
 
 today=$(date +%F)
 
 ottoDir=/hive/data/outside/otto/sarscov2phylo
 cogUrlBase=https://cog-uk.s3.climb.ac.uk/phylogenetics/latest
 
 mkdir -p $ottoDir/cogUk.$today
 cd $ottoDir/cogUk.$today
 
 curl -S -s $cogUrlBase/cog_all.fasta | xz -T 50 > cog_all.fasta.xz
 curl -S -s $cogUrlBase/cog_metadata.csv > cog_metadata.csv
+curl -S -s $cogUrlBase/cog_global_tree.newick > cog_global_tree.newick
 
 tail -n +2 cog_metadata.csv \
 | awk -F, '{print $1 "\t" $4;}' | sort > cogUkToDate
 
 rm -f $ottoDir/cogUk.latest
 ln -s cogUk.$today $ottoDir/cogUk.latest