d02449d1394960b2bc3e6f0de73ad6ae32458456
hiram
  Wed Apr 8 14:09:17 2026 -0700
minor issues noted from claude code review refs #36957

diff --git src/hg/makeDb/doc/evaSnp8.txt src/hg/makeDb/doc/evaSnp8.txt
index f56819bee79..aacdf0e3586 100644
--- src/hg/makeDb/doc/evaSnp8.txt
+++ src/hg/makeDb/doc/evaSnp8.txt
@@ -1,124 +1,126 @@
 # Track for EVA snp release 8  - https://www.ebi.ac.uk/eva/?RS-Release&releaseVersion=8
 # Tracks built by Lou on 10/21/2025
 
 # Track was built for the following 41 assemblies
 
 # The GCA accession on the eva release by accession list (https://ftp.ebi.ac.uk/pub/databases/eva/rs_releases/release_8/by_assembly/)
 # were compared to all native assemblies we have. In total there are 945,193,664 variants
 
 # All assemblies were passed by the python pipeline described below
 # Some assemblies had errors and were skipped, more info in RM #36512
 
 # All files were created with the following python3 script:
 
 ~/kent/src/hg/makeDb/scripts/evaSnp/evaSnp8.py
 
 #Then symlinks were made for all databases
 
 for dbs in $(cat /hive/data/outside/eva8/assemblyReleaseList.txt);
 do
 ln -s /hive/data/outside/eva8/$dbs/evaSnp8.bb /gbdb/$dbs/bbi/;
 done
 
 ####################################################################
 ###  adding these contrib tracks to the GenArk browsers
-###   Hiram and Lou - 2026-05-03
+###   Hiram and Lou - 2026-04-03
 
 mkdir /hive/data/outside/genark/evaSnp8
 cd /hive/data/outside/genark/evaSnp8
 ln -s /hive/data/outside/eva8/contributedTracks ./contributedTracks
 
 # make a single generic trackDb.txt file:
 
 sed -e 's#^bigDataUrl #bigDataUrl contrib/evaSnp8/#;
 s#^html #html contrib/evaSnp8/#;' \
   contributedTracks/GCF_905237075.1/trackDb.txt \
    | sed '5a\
 group varRep
 ' > evaSnp8.trackDb.txt
 
 ### then run this script to make the symlinks into the GenArk build directories
 
 #!/bin/bash
 
 ls -dd contributedTracks/GC* | sed -e 's#contributedTracks/##;' | while read acc
 do
   gcX="${acc:0:3}"
   d0="${acc:4:3}"
   d1="${acc:7:3}"
   d2="${acc:10:3}"
   P="${gcX}/${d0}/${d1}/${d2}/${acc}"
   aB="genbankBuild"
   if [ "${gcX}" = "GCF" ]; then
     aB="refseqBuild"
   fi
   buildPath=`ls -d /hive/data/genomes/asmHubs/$aB/${P}*`
   if [ -d "${buildPath}" ]; then
      mkdir -p "${buildPath}/contrib/evaSnp8"
      for F in evaSnp8.bb description.html
      do
        rm -f "${buildPath}/contrib/evaSnp8/${F}"
        ln -s `pwd -P`/contributedTracks/${acc}/${F} "${buildPath}/contrib/evaSnp8"
      done
      rm -f "${buildPath}/contrib/evaSnp8/evaSnp8.trackDb.txt"
      ln -s `pwd -P`/evaSnp8.trackDb.txt "${buildPath}/contrib/evaSnp8/evaSnp8.trackDb.txt"
      printf "%s\n" "${acc}"
   else
      printf "ERROR: Not found:\n%s\n" "${buildPath}" 1>&2
   fi
 done
 
 ### that is in the mkLinks.sh script:
 
   time (./mkLinks.sh) > do.log 2>&1
 
 ### Then add evaSnp8 to the trackDb/betaGenArk.txt file in the source tree:
 
 cat ~/kent/src/hg/makeDb/trackDb/betaGenArk.txt
 
 # the listing in this file triggers the building of the beta.hub.txt
 # file in the genark system.  Any contrib project listed here will be included
 # contrib track name: tracks found in <buildDir>/contrib/<thisName>/
 tiberius
 VEuPathDB
 TOGAv2
 evaSnp8
 
 ### and then, in each GenArk 'clade' directory that has these
 ### assemblies: in the source tree: kent/src/hg/makeDb/doc
 ### obtained by taking the list of accessions from the 'do.log' from
 ###  the mkLinks.sh output to find which directories have these assemblies:
 
     grep -l -F -f do.log *AsmHub/*orderList.tsv
 
 ### resulting directory list:
 
+cd ~/kent/src/hg/makeDb/doc
 for D in plantsAsmHub birdsAsmHub fishAsmHub primatesAsmHub legacyAsmHub mammalsAsmHub invertebrateAsmHub fungiAsmHub bacteriaAsmHub
 do
   cd "${D}"
   time (make) > dbg 2>&1
   egrep --color=auto -i "error|fail|missing|cannot|clade|class|real" dbg
   time (make verifyTestDownload) >> test.down.log 2>&1
   egrep --color=auto -i "error|fail|missing|cannot|clade|class|real" test.down.log
   time (make sendDownload) >> send.down.log 2>&1
   egrep --color=auto -i "error|fail|missing|cannot|clade|class|real" send.down.log
   time (make verifyDownload) >> verify.down.log 2>&1
   egrep --color=auto -i "error|fail|missing|cannot|clade|class|real" verify.down.log
+  cd ~/kent/src/hg/makeDb/doc
 done
 
 ### In practice, that set of four 'make' commands are run in parallel in each
 ### of the 'clade' directories.  Thus, running 'time (make) > dbg' first
 ### in each directory, then verifyTestDownload in each and so forth.
 ###  it takes a while to run those things in the directories with the
 ###  large *.orderList.tsv files
 ### i.e. wc -l on each one:
 #	444 plantsAsmHub/plants.orderList.tsv
 #	543 birdsAsmHub/birds.orderList.tsv
 #	634 fishAsmHub/fish.orderList.tsv
 #	616 primatesAsmHub/primates.orderList.tsv
 #	689 legacyAsmHub/legacy.orderList.tsv
 #	836 mammalsAsmHub/mammals.orderList.tsv
 #	1941 invertebrateAsmHub/invertebrate.orderList.tsv
 #	4128 fungiAsmHub/fungi.orderList.tsv
 #	22332 bacteriaAsmHub/bacteria.orderList.tsv
 #############################################################################