e6d4c01b643aaaf0aea8d0cbc7fbd1ca7cb76232
angie
  Fri Dec 20 15:42:16 2024 -0800
Use /dev/shm as TMPDIR; new compute nodes don't set it and don't have /data/tmp.

diff --git src/hg/utils/otto/sarscov2phylo/runPangolin.sh src/hg/utils/otto/sarscov2phylo/runPangolin.sh
index 82a25ef..01f73e3 100755
--- src/hg/utils/otto/sarscov2phylo/runPangolin.sh
+++ src/hg/utils/otto/sarscov2phylo/runPangolin.sh
@@ -1,16 +1,18 @@
 #!/bin/bash
 source ~/.bashrc
 conda activate pangolin
 set -beEu -x -o pipefail
 
+export TMPDIR=/dev/shm
+
 # Run pangolin/pangoLEARN on a file (not pipe) and output full CSV
 # (suitable for cluster run on faSplit sequence chunks)
 
 fa=$1
 out=$fa.pangolin.csv
 
 threadCount=6
 
 logfile=$(mktemp)
 pangolin -t $threadCount --skip-scorpio $fa --outfile $out > $logfile 2>&1
 rm $logfile