e22c5be5fb552757c886e7356db9d49eca8cdedb
angie
  Thu Jun 18 15:13:24 2026 -0700
Use TMPDIR -- this no longer runs on hgwdev.

diff --git src/hg/utils/otto/fluA/updateAndersenLab.sh src/hg/utils/otto/fluA/updateAndersenLab.sh
index d320013ba93..91c0469de60 100755
--- src/hg/utils/otto/fluA/updateAndersenLab.sh
+++ src/hg/utils/otto/fluA/updateAndersenLab.sh
@@ -1,32 +1,36 @@
 #!/bin/bash
 set -beEu -o pipefail
 
 export PATH=~/bin/x86_64:~/bin/scripts:$PATH
 fluADir=/hive/data/outside/otto/fluA
 
+if [[ ! -v TMPDIR ]]; then
+    export TMPDIR=/scratch/tmp
+fi
+
 # Update Andersen Lab avian-influenza repo (assemblies of USDA H5N1 sequences) and map by name
 # to GenBank seqs
 cd ~/github/avian-influenza
 git pull
 ./scripts/map_genbank.sh ~/github/avian-influenza/metadata/SraRunTable_automated.csv \
     ~/github/avian-influenza/fasta \
-    > /data/tmp/angie/genbank_mapping.tsv
+    > $TMPDIR/genbank_mapping.tsv
 
-wc -l /data/tmp/angie/genbank_mapping.tsv
+wc -l $TMPDIR/genbank_mapping.tsv
 
-cd /data/tmp/angie
+cd $TMPDIR
 
 # Extract sequences that are in SRA but not (yet) in GenBank.
 find ~/github/avian-influenza/fasta -name \*.fa \
 | grep -vFwf <(cut -f 1 genbank_mapping.tsv) \
 | xargs cat > sraNotGb.fa
 faSize sraNotGb.fa | head -2
 
 # Rename those sequences to look nicer in the tree and include some metadata.
 csvToTab < ~/github/avian-influenza/metadata/SraRunTable_automated.csv \
 | tail -n+2 \
 | cut -f 1,10,16,19,31 \
 | perl -wne 'chomp;
     ($run, $date, $country, $host, $sample) = split(/\t/);
     $year = $date;  $year =~ s/^(\d{4}).*/$1/;
     $host = ucfirst(lc($host));