562a5ca722b958707b6ac1033d5dec067da96736
angie
  Sat Jan 23 14:25:01 2021 -0800
Add source ~/.bashrc at beginning.  Not sure why that was not necessary before but is now.

diff --git src/hg/utils/otto/nextstrainNcov/doUpdate.sh src/hg/utils/otto/nextstrainNcov/doUpdate.sh
index 441daa9..1f582aa 100755
--- src/hg/utils/otto/nextstrainNcov/doUpdate.sh
+++ src/hg/utils/otto/nextstrainNcov/doUpdate.sh
@@ -1,16 +1,17 @@
 #!/bin/bash
+source ~/.bashrc
 set -beEu -o pipefail
 
 #	Do not modify this script, modify the source tree copy:
 #	kent/src/hg/utils/nextstrainNcov/doUpdate.sh
 
 ottoDir=/hive/data/outside/otto/nextstrainNcov
 chromSizes=/hive/data/genomes/wuhCor1/chrom.sizes
 gbdbDir=/gbdb/wuhCor1/nextstrain
 
 ncovJsonUrl='https://nextstrain.org/charon/getDataset?prefix=/ncov/global'
 
 cd $ottoDir
 
 # The file is named .json, but is actually gzipped, so gunzip it.
 rm -f ncov.json