b2702356792837c28408c0dc239c42f066f02e06
angie
  Tue Nov 2 13:03:26 2021 -0700
Helper script for running Pangolin on the cluster.

diff --git src/hg/utils/otto/sarscov2phylo/runPangolin.sh src/hg/utils/otto/sarscov2phylo/runPangolin.sh
new file mode 100755
index 0000000..836ce41
--- /dev/null
+++ src/hg/utils/otto/sarscov2phylo/runPangolin.sh
@@ -0,0 +1,10 @@
+#!/bin/bash
+source ~/.bashrc
+conda activate pangolin
+set -beEu -o pipefail
+
+fa=$1
+out=$fa.pangolin.csv
+logfile=$(mktemp)
+pangolin $fa --outfile $out > $logfile 2>&1
+rm $logfile