2a551773f1cca84e8acb73cf1856f78111d53002
angie
  Fri Jan 22 10:57:17 2021 -0800
Use curl not wget to avoid annoying .1, .2 files on retries.

diff --git src/hg/utils/otto/sarscov2phylo/getCogUk.sh src/hg/utils/otto/sarscov2phylo/getCogUk.sh
index ab711c7..b2affda 100755
--- src/hg/utils/otto/sarscov2phylo/getCogUk.sh
+++ src/hg/utils/otto/sarscov2phylo/getCogUk.sh
@@ -1,27 +1,25 @@
 #!/bin/bash
 
 set -beEux -o pipefail
 
 # 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
 
-wget -q $cogUrlBase/cog_all.fasta
-wget -q $cogUrlBase/cog_metadata.csv
-
-xz -f -T 50 cog_all.fasta
+curl -S -s $cogUrlBase/cog_all.fasta | xz -T 50 > cog_all.fasta.xz
+curl -S -s $cogUrlBase/cog_metadata.csv > cog_metadata.csv
 
 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