dc8ad8ee1ee8372436d900053d1c37c9f1f77425
hiram
  Fri Jul 14 10:06:07 2023 -0700
adding GCA_016920875.1_Utah_Ccol_1.0 slender pigeon louse (jgb_00001 2021) per user request and make the cp -p statements safe refs #29545

diff --git src/hg/makeDb/doc/asmHubs/asmHubs.mk src/hg/makeDb/doc/asmHubs/asmHubs.mk
index 383db7d..392773c 100644
--- src/hg/makeDb/doc/asmHubs/asmHubs.mk
+++ src/hg/makeDb/doc/asmHubs/asmHubs.mk
@@ -19,30 +19,31 @@
 	mkdir -p ${destDir}
 
 sshKeyDownload:
 	ssh -o PasswordAuthentication=no qateam@hgdownload 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::
 	@printf "# starting mkGenomes " 1>&2
 	@date "+%s %F %T" 1>&2
 	${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} ; \
 done
 
@@ -65,30 +66,31 @@
 	${toolsDir}/trackData.pl ${Name} ${name} ${orderList} > ${destDir}/download.${dataName}.html
 	${toolsDir}/trackData.pl -test ${Name} ${name} ${orderList} > ${destDir}/${dataName}.html
 	chmod +x ${destDir}/${dataName}.html
 	chmod +x ${destDir}/download.${dataName}.html
 
 indexPages: hubIndex asmStats trackData
 	echo indexPages done
 
 hubTxt:
 	rm -f ${destDir}/${testHubFile}.txt ${destDir}/${hubFile}.txt
 	sed -e "s#index.html#${indexName}.html#; s#genomes.txt#${genomesTxt}.txt#;" ${srcDir}/${hubTxtFile} > ${destDir}/${hubFile}.txt
 
 # all hubs have the same set of groups, no need for any name customization
 groupsTxt:
 	rm -f ${destDir}/groups.txt
+	rm -f ${destDir}/groups.txt
 	cp -p ${toolsDir}/groups.txt ${destDir}/groups.txt
 
 clean::
 	rm -f ${destDir}/${hubFile}.txt
 	rm -f ${destDir}/${testHubFile}.txt
 	rm -f ${destDir}/groups.txt
 	rm -f ${destDir}/${genomesTxt}.txt
 	rm -f ${destDir}/${indexName}.html
 	rm -f ${destDir}/${testIndexName}.html
 	rm -f ${destDir}/${statsName}.html
 	rm -f ${destDir}/${testStatsName}.html
 
 sendDownload:: sshKeyCheck
 	${toolsDir}/mkSendList.pl ${orderList} | while read F; do \
 	  ${toolsDir}/sendToHgdownload.sh $$F < /dev/null; done