50d655bec99c9e0a4f201ced82513d4c936af575
hiram
  Wed Mar 3 20:14:44 2021 -0800
now creating useOneFile hub.txt files for each individual hub and separate files for download and adding blat servers for hubs on hgwdev refs #26658

diff --git src/hg/makeDb/doc/asmHubs/asmHubs.mk src/hg/makeDb/doc/asmHubs/asmHubs.mk
index 3b23af5..6e30bd1 100644
--- src/hg/makeDb/doc/asmHubs/asmHubs.mk
+++ src/hg/makeDb/doc/asmHubs/asmHubs.mk
@@ -1,68 +1,97 @@
 # generic makefile to construct the index pages and symlinks
 # for any assembly hub
 #
 # will be included by those individual build directories with the
 # following variables defined to customize the resulting files:
 #
 # destDir, srcDir, orderList, indexName, testIndexName,
 # statsName, testStatsName, dataName, testDataName, genomesTxt, hubFile
 # testHubFile, Name and name
 
 toolsDir=${HOME}/kent/src/hg/makeDb/doc/asmHubs
+htdocsHgDownload=/usr/local/apache/htdocs-hgdownload
+hubsDownload=${htdocsHgDownload}/hubs/${name}
+asmHubSrc=/hive/data/genomes/asmHubs/${name}
 
 all:: makeDirs mkGenomes symLinks hubIndex asmStats trackData hubTxt groupsTxt
 
 makeDirs:
 	mkdir -p ${destDir}
 
 mkGenomes::
-	${toolsDir}/mkGenomes.pl ${orderList} > ${destDir}/${genomesTxt}.txt
+	${toolsDir}/mkGenomes.pl localhost 4040 ${orderList} > ${destDir}/${genomesTxt}.txt
+	${toolsDir}/mkGenomes.pl hgwdev 4040 ${orderList} > ${destDir}/download.${genomesTxt}.txt
 
 symLinks::
 	${toolsDir}/mkSymLinks.pl ${orderList}
+	@[ -d ${hubsDownload} ] && true || mkdir ${hubsDownload}
+	@for html in index asmStats trackData ; 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
 
 hubIndex::
-	${toolsDir}/mkHubIndex.pl ${Name} ${name} ${defaultAssembly} ${orderList} | sed -e 's#${name}/hub.txt#${name}/${hubFile}.txt#;' > ${destDir}/${indexName}.html
-	sed -e "s#genome.ucsc.edu/h/#genome-test.gi.ucsc.edu/h/#g; s/hgdownload.soe/hgdownload-test.gi/g; s#/${indexName}.html#/${testIndexName}.html#; s#${name}/${hubFile}.txt#${name}/${testHubFile}.txt#; s/${statsName}.html/${testStatsName}.html/; s#${dataName}.html#${testDataName}.html#;" ${destDir}/${indexName}.html > ${destDir}/${testIndexName}.html
-	chmod +x ${destDir}/${indexName}.html ${destDir}/${testIndexName}.html
+	rm -f ${destDir}/${testIndexName}.html ${destDir}/${indexName}.html ${destDir}/download.${indexName}.html
+	${toolsDir}/mkHubIndex.pl ${Name} ${name} ${defaultAssembly} ${orderList} | sed -e 's#${name}/hub.txt#${name}/${hubFile}.txt#;' > ${destDir}/download.${indexName}.html
+	sed -e "s#genome.ucsc.edu/h/#genome-test.gi.ucsc.edu/h/#g; s/hgdownload.soe/hgdownload-test.gi/g;" ${destDir}/download.${indexName}.html > ${destDir}/${indexName}.html
+	chmod +x ${destDir}/${indexName}.html ${destDir}/download.${indexName}.html
 
 asmStats::
-	rm -f ${destDir}/${statsName}.html ${destDir}/${testStatsName}.html
-	${toolsDir}/mkAsmStats.pl ${Name} ${name} ${orderList} > ${destDir}/${statsName}.html
-	sed -e "s#genome.ucsc.edu/h/#genome-test.gi.ucsc.edu/h/#g; s/hgdownload.soe/hgdownload-test.gi/g; s/${indexName}.html/${testIndexName}.html/; s#/${statsName}.html#/${testStatsName}.html#; s#${dataName}.html#${testDataName}.html#;" ${destDir}/${statsName}.html > ${destDir}/${testStatsName}.html
-	chmod +x ${destDir}/${statsName}.html ${destDir}/${testStatsName}.html
+	rm -f ${destDir}/download.${statsName}.html ${destDir}/${statsName}.html ${destDir}/${testStatsName}.html
+	${toolsDir}/mkAsmStats.pl ${Name} ${name} ${orderList} > ${destDir}/download.${statsName}.html
+	sed -e "s#genome.ucsc.edu/h/#genome-test.gi.ucsc.edu/h/#g; s/hgdownload.soe/hgdownload-test.gi/g;" ${destDir}/download.${statsName}.html > ${destDir}/${statsName}.html
+	chmod +x ${destDir}/${statsName}.html ${destDir}/download.${statsName}.html
 
 # trackData makes different tables for the test vs. production version
 # mkHubIndex.pl and mkAsmStats.pl should do this too . . .  TBD
 trackData::
-	${toolsDir}/trackData.pl ${Name} ${name} ${orderList} > ${destDir}/${dataName}.html
-	${toolsDir}/trackData.pl -test ${Name} ${name} ${orderList} | sed -e "s#${indexName}.html#${testIndexName}.html#; s#${statsName}.html#${testStatsName}.html#; s#${dataName}.html#${testDataName}.html#;" > ${destDir}/${testDataName}.html
+	rm -f ${destDir}/${testDataName}.html ${destDir}/${dataName}.html ${destDir}/download.${dataName}.html
+	${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 ${destDir}/${testDataName}.html
+	chmod +x ${destDir}/download.${dataName}.html
 
 hubTxt:
-	rm -f ${destDir}/${hubFile}.txt
+	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
-	sed -e 's/index.html/${testIndexName}.html/; s#genomes.txt#${genomesTxt}.txt#;' ${srcDir}/${hubTxtFile} > ${destDir}/${testHubFile}.txt
 
 # all hubs have the same set of groups, no need for any name customization
 groupsTxt:
 	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::
 	${toolsDir}/mkSendList.pl ${orderList} | while read F; do \
 	  ${toolsDir}/sendToHgdownload.sh $$F < /dev/null; done
-	rsync -L -a -P --exclude 'test*' \
-	    /usr/local/apache/htdocs-hgdownload/hubs/${name}/ \
+	rsync -L -a -P \
+  /usr/local/apache/htdocs-hgdownload/hubs/${name}/groups.txt \
+		qateam@hgdownload:/mirrordata/hubs/${name}/
+	rsync -L -a -P \
+  /usr/local/apache/htdocs-hgdownload/hubs/${name}/${hubFile}.txt \
 		qateam@hgdownload:/mirrordata/hubs/${name}/
+	rsync -L -a -P \
+  /usr/local/apache/htdocs-hgdownload/hubs/${name}/download.${indexName}.html \
+		qateam@hgdownload:/mirrordata/hubs/${name}/${indexName}.html
+	rsync -L -a -P \
+  /usr/local/apache/htdocs-hgdownload/hubs/${name}/download.${statsName}.html \
+		qateam@hgdownload:/mirrordata/hubs/${name}/${statsName}.html
+	rsync -L -a -P \
+  /usr/local/apache/htdocs-hgdownload/hubs/${name}/download.${dataName}.html \
+		qateam@hgdownload:/mirrordata/hubs/${name}/${dataName}.html
+	rsync -L -a -P \
+  /usr/local/apache/htdocs-hgdownload/hubs/${name}/download.${genomesTxt}.txt \
+		qateam@hgdownload:/mirrordata/hubs/${name}/${genomesTxt}.txt
+