6c8734919a8bbcc7b0ef17a89ef86d21d80686cb
hiram
  Thu Jan 23 14:25:13 2020 -0800
now using a minimal makefile and common scripts to make any assembly hub refs #24748

diff --git src/hg/makeDb/doc/asmHubs/asmHubs.mk src/hg/makeDb/doc/asmHubs/asmHubs.mk
index c8dc51c..e32955d 100644
--- src/hg/makeDb/doc/asmHubs/asmHubs.mk
+++ src/hg/makeDb/doc/asmHubs/asmHubs.mk
@@ -2,43 +2,40 @@
 # for any of the assembly hubs:
 # primates, mammals, birds, fish, vertebrate
 #
 # will be included by those individual build directories with the
 # Name and name defined to use here
 
 destDir=/hive/data/genomes/asmHubs/${name}
 srcDir=${HOME}/kent/src/hg/makeDb/doc/${name}AsmHub
 toolsDir=${HOME}/kent/src/hg/makeDb/doc/asmHubs
 
 all:: makeDirs ${destDir}/hub.txt ${destDir}/groups.txt ${destDir}/genomes.txt \
 	${destDir}/index.html ${destDir}/asmStats${Name}.html
 
 makeDirs:
 	mkdir -p ${destDir}
-	${srcDir}/mkSymLinks.pl
+	${toolsDir}/mkSymLinks.pl ${Name} ${name}
 
-${destDir}/index.html: ${srcDir}/mkHubIndex.pl
-	${srcDir}/mkHubIndex.pl > $@
+${destDir}/index.html: ${toolsDir}/mkHubIndex.pl
+	${toolsDir}/mkHubIndex.pl ${Name} ${name} ${defaultAssembly} > $@
 	sed -e "s/hgdownload.soe/genome-test.gi/g; s#/index.html#/testIndex.html#; s#${name}/hub.txt#${name}/testHub.txt#; s/asmStats${Name}/testAsmStats${Name}/;" $@ > ${destDir}/testIndex.html
 	chmod +x $@ ${destDir}/testIndex.html
 
 ${destDir}/asmStats${Name}.html: ${toolsDir}/mkAsmStats.pl
 	${toolsDir}/mkAsmStats.pl ${Name} ${name} > $@
-	sed -e "s/hgdownload.soe/genome-test.gi/g; s/index.html/testIndex.html/; s/asmStats${Name}/testAsmStats${Name}/;" $@ > ${destDir}/testAsmStats${Name}.html
+	sed -e "s/hgdownload.soe/genome-test.gi/g; s/index.html/testIndex.html/; s#/asmStats#/testAsmStats#;" $@ > ${destDir}/testAsmStats${Name}.html
 	chmod +x $@ ${destDir}/testAsmStats${Name}.html
 
-${destDir}/genomes.txt:  ${srcDir}/mkGenomes.pl \
-	${srcDir}/${name}.asmId.commonName.tsv \
-	${srcDir}/${name}.commonName.asmId.orderList.tsv
-	${srcDir}/mkGenomes.pl > $@
-
-# ${destDir}/genomes.txt:  ${destDir}/asmStats${Name}.html ${srcDir}/mkGenomes.pl ${srcDir}/mkSymLinks.sh
-#	cd ${destDir} && ${srcDir}/mkSymLinks.sh
+${destDir}/genomes.txt:  ${toolsDir}/mkGenomes.pl \
+	${toolsDir}/${name}.asmId.commonName.tsv \
+	${toolsDir}/${name}.commonName.asmId.orderList.tsv
+	${toolsDir}/mkGenomes.pl ${Name} ${name} > $@
 
 ${destDir}/hub.txt: ${srcDir}/hub.txt
 	rm -f ${destDir}/hub.txt
 	cp -p ${srcDir}/hub.txt ${destDir}/hub.txt
 	sed -e 's/index.html/testIndex.html/;' ${srcDir}/hub.txt > ${destDir}/testHub.txt
 
-${destDir}/groups.txt: ${srcDir}/groups.txt
+${destDir}/groups.txt: ${toolsDir}/groups.txt
 	rm -f ${destDir}/groups.txt
-	cp -p ${srcDir}/groups.txt ${destDir}/groups.txt
+	cp -p ${toolsDir}/groups.txt ${destDir}/groups.txt