6addae8d76b1b44013e1e27762268fb8a8d858b5
hiram
  Thu Apr 10 12:35:47 2025 -0700
correctly make the assemblyList.json for the VGP set refs #34370

diff --git src/hg/makeDb/doc/asmHubs/asmHubs.mk src/hg/makeDb/doc/asmHubs/asmHubs.mk
index a46880d15c0..7be65fb43c6 100644
--- src/hg/makeDb/doc/asmHubs/asmHubs.mk
+++ src/hg/makeDb/doc/asmHubs/asmHubs.mk
@@ -40,31 +40,31 @@
 	fi
 
 sshKeyDownload:
 	ssh -o PasswordAuthentication=no qateam@${downloadDest1} date
 	ssh -o PasswordAuthentication=no qateam@${downloadDest2} date
 	ssh -o PasswordAuthentication=no qateam@${downloadDest3} date
 
 sshKeyDynablat:
 	ssh -o PasswordAuthentication=no qateam@dynablat-01 date
 
 sshKeyCheck: sshKeyDownload sshKeyDynablat
 	@printf "# ssh keys to hgdownload and dynablat-01 are good\n"
 
 mkJson::
 	if [ "$(name)" = "VGP" ]; then \
-	cat *.orderList.tsv | ${toolsDir}/tsvToJson.py stdin > ${destDir}/assemblyList.json 2> ${name}.jsonData.txt; \
+	sort -u *.orderList.tsv | ${toolsDir}/tsvToJson.py stdin > ${destDir}/assemblyList.json 2> ${name}.jsonData.txt; \
 	else \
 	${toolsDir}/tsvToJson.py ${orderList} > ${destDir}/assemblyList.json 2> ${name}.jsonData.txt; \
         fi
 
 # mkGenomes needs symLinks to run before mkGenomes runs, and then
 # the second symLinks after mkGenomes uses business created by mkGenomes
 
 mkGenomes::
 	@printf "# starting mkGenomes " 1>&2
 	${toolsDir}/mkSymLinks.pl ${orderList}
 	@date "+%s %F %T" 1>&2
 	@rm -f hasChainNets.txt
 	${toolsDir}/mkGenomes.pl dynablat-01 4040 ${orderList} > /dev/null
 	@printf "# finished mkGenomes " 1>&2
 	@date "+%s %F %T" 1>&2