06d7be056190c14b85e71bc12523f18ea6815b5e
markd
  Mon Dec 7 00:50:29 2020 -0800
BLAT mmap index support merge with master

diff --git src/hg/utils/otto/sarscov2phylo/getCogUk.sh src/hg/utils/otto/sarscov2phylo/getCogUk.sh
new file mode 100755
index 0000000..d2a2e2c
--- /dev/null
+++ src/hg/utils/otto/sarscov2phylo/getCogUk.sh
@@ -0,0 +1,27 @@
+#!/bin/bash
+
+set -beEu -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
+
+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