06c02db4f03372ffd0d386846d4d9de377a36555
hiram
  Wed Jan 22 14:24:30 2020 -0800
getting the build system for assembly hubs into a single set of files for all categories of hubs refs #24812

diff --git src/hg/makeDb/doc/asmHubs/asmHubs.mk src/hg/makeDb/doc/asmHubs/asmHubs.mk
new file mode 100644
index 0000000..c8dc51c
--- /dev/null
+++ src/hg/makeDb/doc/asmHubs/asmHubs.mk
@@ -0,0 +1,44 @@
+# generic makefile to construct the index pages and symlinks
+# 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}
+	${srcDir}/mkSymLinks.pl
+
+${destDir}/index.html: ${srcDir}/mkHubIndex.pl
+	${srcDir}/mkHubIndex.pl > $@
+	sed -e "s/hgdownload.soe/genome-test.gi/g; s#/index.html#/testIndex.html#; s#${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
+	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}/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
+	rm -f ${destDir}/groups.txt
+	cp -p ${srcDir}/groups.txt ${destDir}/groups.txt