8fd2016b6c0e6a6c0bccbf47f2133124c5e6657e
hiram
  Mon May 20 12:48:30 2024 -0700
this will make symLinks happen twice but it is needed and now making a chain net listing while running refs #29545

diff --git src/hg/makeDb/doc/asmHubs/asmHubs.mk src/hg/makeDb/doc/asmHubs/asmHubs.mk
index c293fa7..eca83f4 100644
--- src/hg/makeDb/doc/asmHubs/asmHubs.mk
+++ src/hg/makeDb/doc/asmHubs/asmHubs.mk
@@ -28,33 +28,34 @@
 	    echo "ERROR: duplicate accession in '$$tsvFile'"; \
 	    cut -d'_' -f1-2 ${orderList} | sort | uniq -c | awk '$$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"
 
-mkGenomes::
+mkGenomes:: symLinks
 	@printf "# starting mkGenomes " 1>&2
 	@date "+%s %F %T" 1>&2
+	@rm -f hasChainNets.txt
 	${toolsDir}/mkGenomes.pl dynablat-01 4040 ${orderList} > ${destDir}/${genomesTxt}.txt
 	rm -f ${destDir}/download.${genomesTxt}.txt
 	cp -p ${destDir}/${genomesTxt}.txt ${destDir}/download.${genomesTxt}.txt
 	@printf "# finished mkGenomes " 1>&2
 	@date "+%s %F %T" 1>&2
 
 symLinks::
 	${toolsDir}/mkSymLinks.pl ${orderList}
 	@[ -d ${hubsDownload} ] && true || mkdir ${hubsDownload}
 	@for html in ${indexName} ${statsName} ${dataName} ; do \
 [ -L ${hubsDownload}/$${html}.html ] && true || ln -s ${asmHubSrc}/$${html}.html ${hubsDownload} ; \
 [ -L ${hubsDownload}/download.$${html}.html ] && true || ln -s ${asmHubSrc}/download.$${html}.html ${hubsDownload} ; \
 done
 	@for txt in groups hub genomes download.genomes ; do \
 [ -L ${hubsDownload}/$${txt}.txt ] && true || ln -s ${asmHubSrc}/$${txt}.txt ${hubsDownload} ; \