acd9854d3c6537ff237c597534abd5b9afbb7a75
angie
  Thu Feb 25 10:40:45 2021 -0800
Adding cron scripts for nightly update of public tree, VCFs, metadata and protobufs for hgPhyloPlace.

diff --git src/hg/utils/otto/sarscov2phylo/pangolinNcbi.sh src/hg/utils/otto/sarscov2phylo/pangolinNcbi.sh
new file mode 100755
index 0000000..36d3512
--- /dev/null
+++ src/hg/utils/otto/sarscov2phylo/pangolinNcbi.sh
@@ -0,0 +1,16 @@
+#!/bin/bash
+# Don't exit on error, just attempt to run pangolin on ncbi.latest
+
+#	Do not modify this script, modify the source tree copy:
+#	kent/src/hg/utils/otto/sarscov2phylo/pangolinNcbi.sh
+
+ottoDir=/hive/data/outside/otto/sarscov2phylo
+ncbiDir=$ottoDir/ncbi.latest
+
+cd $ncbiDir
+
+source ~/.bashrc
+conda activate pangolin
+pangolin <(xzcat genbank.fa.xz) >& pangolin.log
+
+exit 0