be4311c07e14feb728abc6425ee606ffaa611a58
markd
  Fri Jan 22 06:46:58 2021 -0800
merge with master

diff --git src/hg/utils/otto/sarscov2phylo/installSarsCov2Phylo.sh src/hg/utils/otto/sarscov2phylo/installSarsCov2Phylo.sh
new file mode 100755
index 0000000..e41cf44
--- /dev/null
+++ src/hg/utils/otto/sarscov2phylo/installSarsCov2Phylo.sh
@@ -0,0 +1,80 @@
+#!/bin/bash
+set -beEu -x -o pipefail
+
+#	Do not modify this script, modify the source tree copy:
+#	kent/src/hg/utils/otto/sarscov2phylo/updateSarsCov2Phylo.sh
+
+usage() {
+    echo "usage: $0 releaseLabel"
+}
+
+if [ $# != 1 ]; then
+  usage
+  exit 1
+fi
+
+releaseLabel=$1
+
+ottoDir=/hive/data/outside/otto/sarscov2phylo
+gbdbRoot=/gbdb/wuhCor1
+
+cd $ottoDir/$releaseLabel
+
+# GISAID track
+for f in gisaid-${releaseLabel}{,.minAf.01,.minAf.001}.vcf.gz; do
+    if [ ! -f $f ]; then
+        echo "File '$f' not found"
+        #*** exit 1
+    fi
+    if [ ! -f $f.tbi ]; then
+        echo "File '$f.tbi' not found"
+        #*** exit 1
+    fi
+    t=$(echo $f | sed -re "s/-$releaseLabel//")
+    ln -sf $ottoDir/$releaseLabel/$f $gbdbRoot/sarsCov2Phylo/$t
+    ln -sf $ottoDir/$releaseLabel/$f.tbi $gbdbRoot/sarsCov2Phylo/$t.tbi
+done
+ln -sf $ottoDir/$releaseLabel/gisaid-$releaseLabel.parsimony.bw \
+    $gbdbRoot/sarsCov2Phylo/gisaid.parsimony.bw
+
+ln -sf $ottoDir/$releaseLabel/global.reroot.collapsed.nwk $gbdbRoot/sarsCov2Phylo/
+
+for f in {gisaid,lineage,nextstrain}Colors.gz; do
+    ln -sf $ottoDir/$releaseLabel/$f $gbdbRoot/sarsCov2Phylo/sarscov2phylo.$f
+done
+
+echo "$releaseLabel" > sarscov2phylo-$releaseLabel.version.txt
+ln -sf $ottoDir/$releaseLabel/sarscov2phylo-$releaseLabel.version.txt \
+    $gbdbRoot/sarsCov2Phylo/sarscov2phylo.version.txt
+
+# Public track
+for f in public-$releaseLabel{,.all}{,.minAf.01,.minAf.001}.vcf.gz; do
+    if [ ! -f $f ]; then
+        echo "File '$f' not found"
+        #*** exit 1
+    fi
+    if [ ! -f $f.tbi ]; then
+        echo "File '$f.tbi' not found"
+        #*** exit 1
+    fi
+    t=$(echo $f | sed -re "s/-$releaseLabel//")
+    ln -sf $ottoDir/$releaseLabel/$f $gbdbRoot/sarsCov2PhyloPub/$t
+    ln -sf $ottoDir/$releaseLabel/$f.tbi $gbdbRoot/sarsCov2PhyloPub/$t.tbi
+done
+for s in {,.all}.parsimony.bw; do
+    ln -sf $ottoDir/$releaseLabel/public-$releaseLabel$s $gbdbRoot/sarsCov2PhyloPub/public$s
+done
+
+ln -sf $ottoDir/$releaseLabel/global.reroot.collapsed.public-$releaseLabel.nwk \
+    $gbdbRoot/sarsCov2PhyloPub/sarscov2phylo.pub.ft.nh
+
+ln -sf $ottoDir/$releaseLabel/public-$releaseLabel.all.nwk \
+    $gbdbRoot/sarsCov2PhyloPub/sarscov2phylo.pub.all.ft.nh
+
+for f in public{Gisaid,Lineage,Nextstrain}Colors.gz; do
+    t=$(echo $f | sed -re 's/^public([A-Z])/\l\1/')
+    ln -sf $ottoDir/$releaseLabel/$f $gbdbRoot/sarsCov2PhyloPub/sarscov2phylo.pub.$t
+done
+
+ln -sf $ottoDir/$releaseLabel/sarscov2phylo-$releaseLabel.version.txt \
+    $gbdbRoot/sarsCov2PhyloPub/sarscov2phylo.pub.version.txt