de23dd389f8e8e35c41880a85d74e9838a4df8e4
angie
  Thu Jun 18 15:11:49 2026 -0700
ssh to hgwdev for commands that need access to hgwdev-only directories, because these scripts run elsewhere now.  Tweak shell variables usherDir and friends to make it easier to try out different build directories.

diff --git src/hg/utils/otto/dengue/buildTree.sh src/hg/utils/otto/dengue/buildTree.sh
index 9afe9f3b2c1..5e7f9f5a530 100755
--- src/hg/utils/otto/dengue/buildTree.sh
+++ src/hg/utils/otto/dengue/buildTree.sh
@@ -1,33 +1,32 @@
 #!/bin/bash
 source ~/.bashrc
 set -beEu -o pipefail
 
 # Align INSDC sequences to references and build 4 trees, one for each subtype 1-4.
 
 dengueScriptDir=$(dirname "${BASH_SOURCE[0]}")
 
 today=$(date +%F)
 
 dengueDir=/hive/data/outside/otto/dengue
 dengueNcbiDir=$dengueDir/ncbi/ncbi.latest
 
-usherDir=~angie/github/usher
-usherSampled=$usherDir/build/usher-sampled
-usher=$usherDir/build/usher
-matUtils=$usherDir/build/matUtils
-matOptimize=$usherDir/build/matOptimize
+usherDir=~angie/github/usher/build
+usherSampled=$usherDir/usher-sampled
+matUtils=$usherDir/matUtils
+matOptimize=$usherDir/matOptimize
 
 # Subtype 1
 asmAcc1=GCF_000862125.1
 gbff1=$dengueDir/NC_001477.1.gbff
 refFa1=$dengueDir/NC_001477.1.fa
 archiveRoot1=/hive/users/angie/publicTreesDenv1
 
 # Subtype 2
 asmAcc2=GCF_000871845.1
 gbff2=$dengueDir/NC_001474.2.gbff
 refFa2=$dengueDir/NC_001474.2.fa
 archiveRoot2=/hive/users/angie/publicTreesDenv2
 
 # Subtype 3
 asmAcc3=GCF_000866625.1
@@ -184,61 +183,62 @@
         > hgPhyloPlace.description.$subtype.txt
 
     # Make a taxonium view
     usher_to_taxonium --input denv$subtype.$today.pb \
         --metadata denv$subtype.$today.metadata.tsv.gz \
         --columns genbank_accession,country,location,date,authors,Nextclade_lineage \
         --genbank $gbff \
         --name_internal_nodes \
         --title "Dengue subtype "$subtype" $today tree with $sampleCountComma genomes from INSDC" \
         --output denv$subtype.$today.taxonium.jsonl.gz \
         >& usher_to_taxonium.$subtype.log
 
     # Update links in /gbdb
     nc=$(basename $gbff .gbff)
     dir=/gbdb/wuhCor1/hgPhyloPlaceData/dengue/$nc
-    mkdir -p $dir
-    ln -sf $(pwd)/denv$subtype.$today.pb $dir/denv$subtype.latest.pb
-    ln -sf $(pwd)/denv$subtype.$today.metadata.tsv.gz $dir/denv$subtype.latest.metadata.tsv.gz
-    ln -sf $(pwd)/hgPhyloPlace.description.$subtype.txt $dir/denv$subtype.latest.version.txt
+    ssh hgwdev mkdir -p $dir
+    ssh hgwdev ln -sf $(pwd)/denv$subtype.$today.pb $dir/denv$subtype.latest.pb
+    ssh hgwdev ln -sf $(pwd)/denv$subtype.$today.metadata.tsv.gz $dir/denv$subtype.latest.metadata.tsv.gz
+    ssh hgwdev ln -sf $(pwd)/hgPhyloPlace.description.$subtype.txt $dir/denv$subtype.latest.version.txt
 
 
     # Extract Newick and VCF for anyone who wants to download those instead of protobuf
     $matUtils extract -i denv$subtype.$today.pb \
         -t denv$subtype.$today.nwk \
         -v denv$subtype.$today.vcf >& tmp.log
     pigz -p 8 -f denv$subtype.$today.nwk denv$subtype.$today.vcf
 
     # Link to public trees download directory hierarchy
     read y m d < <(echo $today | sed -re 's/-/ /g')
     archive=$archiveRoot/$y/$m/$d
     mkdir -p $archive
     ln -f $(pwd)/denv$subtype.$today.{nwk,vcf,metadata.tsv,taxonium.jsonl}.gz $archive/
     gzip -c denv$subtype.$today.pb > $archive/denv$subtype.$today.pb.gz
     ln -f $(pwd)/hgPhyloPlace.description.$subtype.txt $archive/denv$subtype.$today.version.txt
 
     # Update 'latest' in $archiveRoot
     for f in $archive/denv$subtype.$today.*; do
         latestF=$(echo $(basename $f) | sed -re 's/'$today'/latest/')
         ln -f $f $archiveRoot/$latestF
     done
 
     # Update hgdownload-test link for archive
     asmDir=$(echo $asmAcc \
         | sed -re 's@^(GC[AF])_([0-9]{3})([0-9]{3})([0-9]{3})\.([0-9]+)@\1/\2/\3/\4/\1_\2\3\4.\5@')
-    mkdir -p /data/apache/htdocs-hgdownload/hubs/$asmDir/UShER_DENV-$subtype/$y/$m
-    ln -sf $archive /data/apache/htdocs-hgdownload/hubs/$asmDir/UShER_DENV-$subtype/$y/$m
+    ssh hgwdev ln -sf $archiveRoot/*.latest.* /data/apache/htdocs-hgdownload/hubs/$asmDir/UShER_DENV-$subtype/
     # rsync to hgdownload hubs dir
-    for h in hgdownload1 hgdownload3; do
-        if rsync -a -L --delete /data/apache/htdocs-hgdownload/hubs/$asmDir/UShER_DENV-$subtype/* \
+    for h in hgdownload1 hgdownload2 hgdownload3; do
+        if ssh hgwdev rsync -a -L --delete /data/apache/htdocs-hgdownload/hubs/$asmDir/UShER_DENV-$subtype/* \
                  qateam@$h:/mirrordata/hubs/$asmDir/UShER_DENV-$subtype/; then
             true
         else
             echo ""
             echo "*** rsync to $h failed; disk full? ***"
             echo ""
         fi
     done
 done
 
 rm -f mutation-paths.txt *.pre*.pb final-tree.nh
 nice gzip -f *.log *.tsv move_log* *.stderr samples.*
+
+echo All done.