c6b00020d3775552377ee3fda1a77d9cb39c453d
hiram
  Fri Apr 17 15:16:44 2026 -0700
correct specification for the linearGap and scoreMatrix inputs refs #31811

diff --git src/hg/utils/automation/kegAlignLastz.sh src/hg/utils/automation/kegAlignLastz.sh
index fa7af802c7e..28875950c8b 100755
--- src/hg/utils/automation/kegAlignLastz.sh
+++ src/hg/utils/automation/kegAlignLastz.sh
@@ -366,52 +366,70 @@
         "primate")
            ;;
         "mammal")
            ;;
         "other")
            minScore="5000"
            linearGap="loose"
            ;;
      esac
      ;;
    "other")
       minScore="5000"
       linearGap="loose"
 esac
 
+##########  primate <-> primate  #########################################
 if [ "$tClade" == "primate" -a "$qClade" == "primate" ]; then
 
 export yamlString="# ${tAccId}.${qAccId}.yaml
 TARGET_Sequence:
   class: File
   path: ${tFaGzUrl}
 QUERY_Sequence:
   class: File
   path: ${qFaGzUrl}
 # axtChain options
 axtChainMinScore: ${minScore}
-linear_gap_options.linear_gap: ${linearGap}
+axtChainLinearGap:
+  class: File
+  filetype: txt
+  path: https://genome-test.gi.ucsc.edu/~hiram/galaxy/kegAlign/axtChain.medium.txt
+axtChainScoreScheme:
+  class: File
+  filetype: txt
+  path: https://genome-test.gi.ucsc.edu/~hiram/galaxy/kegAlign/primate-primate.lastz.score.txt
+#    A    C    G    T
+#   90 -330 -236 -356
+# -330  100 -318 -236
+# -236 -318  100 -330
+# -356 -236 -330   90
+#     O=600 E=150
 # lastz options
 xdropX: 910
 ydropY: 15000
 stepZ: 1
 noTransitionT: false
 strand_selectorB: both
-seeding_options.seed_selector: 12of19
+# seeding_options.seed.seed_selector: 12of19 does not get into the process
 hspthreshK: 4500
 gappedthreshL: 4500
 innerH: 2000
+scoringMatrix:
+  class: File
+  filetype: txt
+  path: https://genome-test.gi.ucsc.edu/~hiram/galaxy/kegAlign/primate-primate.lastz.score.txt
 "
 
 export defString="# ${qOrgName} ${Query} vs. ${tOrgName} ${Target}
 BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
 BLASTZ_T=2
 BLASTZ_O=600
 BLASTZ_E=150
 BLASTZ_M=254
 BLASTZ_K=4500
 BLASTZ_Y=15000
 BLASTZ_Q=/hive/data/staging/data/blastz/human_chimp.v2.q
 #       A     C     G     T
 # A    90  -330  -236  -356
 # C  -330   100  -318  -236
 # G  -236  -318   100  -330
@@ -433,69 +451,72 @@
 
 BASE=${buildDir}
 TMPDIR=/dev/shm
 "
 else
 
 export yamlString="# ${target}.${query}.yaml
 TARGET_Sequence:
   class: File
   path: ${tFaGzUrl}
 QUERY_Sequence:
   class: File
   path: ${qFaGzUrl}
 # axtChain options
 axtChainMinScore: ${minScore}
-linear_gap_options.linear_gap: ${linearGap}
+axtChainLinearGap:
+  class: File
+  filetype: txt
+  path: https://genome-test.gi.ucsc.edu/~hiram/galaxy/kegAlign/axtChain.loose.txt
 # lastz options
 xdropX: 910
 ydropY: 9400
 stepZ: 1
 noTransitionT: true
 strand_selectorB: both
-seeding_options.seed_selector: 12of19
+# seeding_options.seed.seed_selector: 12of19 does not get into the process
 hspthreshK: 3000
 gappedthreshL: 3000
 innerH: 2000
 "
 export defString="# ${qOrgName} ${Query} vs. ${tOrgName} ${Target}
 BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
 
 # TARGET: ${tOrgName} ${tOrgDate} ${target}
 SEQ1_DIR=${target2bit}
 SEQ1_LEN=${targetSizes}
 SEQ1_CHUNK=20000000
 SEQ1_LAP=10000
 SEQ1_LIMIT=${seq1Limit}
 
 # QUERY: ${qOrgName} ${qOrgDate} ${query}
 SEQ2_DIR=${query2bit}
 SEQ2_LEN=${querySizes}
 SEQ2_CHUNK=20000000
 SEQ2_LAP=0
 SEQ2_LIMIT=${seq2Limit}
 
 BASE=${buildDir}
 TMPDIR=/dev/shm
 "
 
 fi
 
 ### skip primary alignment if it is already done
 ###  primaryDone == 0 means NOT done yet
 if [ $primaryDone -eq 0 ]; then
-  mkdir "${buildDir}"
+  mkdir -p "${buildDir}"
 
 ### setup the DEF file
 printf "%s" "${defString}" > ${buildDir}/DEF
 ### and the yaml file
 printf "%s" "${yamlString}" > ${buildDir}/${tAccId}.${qAccId}.yaml
 
 ### setup the buildDir/lastzRun.sh script
 printf "#!/bin/bash
 
 set -beEu -o pipefail
 
 export targetDb=\"${tAccId}\"
 export queryDb=\"${qAccId}\"
 export QueryDb=\"${Query}\"