daaa29dc6598c41b9943fe3fdca994ef03186a5c
hiram
  Wed Dec 4 14:43:44 2024 -0800
special rule to make the jsonData for VGP refs #34370

diff --git src/hg/makeDb/doc/asmHubs/asmHubs.mk src/hg/makeDb/doc/asmHubs/asmHubs.mk
index 19604f7..885f399 100644
--- src/hg/makeDb/doc/asmHubs/asmHubs.mk
+++ src/hg/makeDb/doc/asmHubs/asmHubs.mk
@@ -35,31 +35,35 @@
 	    cut -d'_' -f1-2 ${orderList} | sort | uniq -c | awk '$$1 > 1'; \
 	    exit 255; \
 	fi
 
 sshKeyDownload:
 	ssh -o PasswordAuthentication=no qateam@${downloadDest1} date
 	ssh -o PasswordAuthentication=no qateam@${downloadDest2} 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::
-	${toolsDir}/tsvToJson.py ${orderList} > ${destDir}/assemblyList.json 2> ${name}.jsonData.txt
+	if [ "$(name)" = "VGP" ]; then \
+	cat *.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
 
 # temporary mkGenomes to get the single file genomes.txt made on a special
 # one time only static list