a501a677b1027e7103b547e54b0e2ee286ca09e7
angie
  Fri Mar 5 15:39:35 2021 -0800
Make getNcbi.sh more efficient: fetch only new IDs from BioSample; run nextclade and pangolin only on new sequences.

diff --git src/hg/utils/otto/sarscov2phylo/pangolinNcbi.sh src/hg/utils/otto/sarscov2phylo/pangolinNcbi.sh
deleted file mode 100755
index 36d3512..0000000
--- src/hg/utils/otto/sarscov2phylo/pangolinNcbi.sh
+++ /dev/null
@@ -1,16 +0,0 @@
-#!/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