5f4eafca0ff4189014f9a214ef0ddbf99ccb6a11
hiram
  Tue Apr 12 14:14:58 2022 -0700
now with rsync pushing refs #29203

diff --git src/hg/makeDb/doc/chm13v2.0/makefile src/hg/makeDb/doc/chm13v2.0/makefile
index 865f669..522aea8 100644
--- src/hg/makeDb/doc/chm13v2.0/makefile
+++ src/hg/makeDb/doc/chm13v2.0/makefile
@@ -1,16 +1,22 @@
 
+asmId = GCA_009914755.4_T2T-CHM13v2.0
+accession = GCA_009914755.4
+stageDir = /hive/data/genomes/asmHubs/genbankBuild/GCA/009/914/755/${asmId}
+pushFromDir = /hive/data/genomes/asmHubs//GCA/009/914/755/${accession}
+pushToDir = /mirrordata/hubs/GCA/009/914/755/${accession}
+
 # default set of hub track html description files
 
 htmlFiles = html/GCA_009914755.4_T2T-CHM13v2.0.assembly.html \
 html/GCA_009914755.4_T2T-CHM13v2.0.chainNet.html \
 html/GCA_009914755.4_T2T-CHM13v2.0.cpgIslands.html \
 html/GCA_009914755.4_T2T-CHM13v2.0.description.html \
 html/GCA_009914755.4_T2T-CHM13v2.0.gc5Base.html \
 html/GCA_009914755.4_T2T-CHM13v2.0.repeatMasker.html \
 html/GCA_009914755.4_T2T-CHM13v2.0.simpleRepeat.html \
 html/GCA_009914755.4_T2T-CHM13v2.0.windowMasker.html \
 html/GCA_009914755.4_T2T-CHM13v2.0.xenoRefGene.html
 
 # these html files come from the T2T porting project, not maintained here
 outsideSource = GCA_009914755.4_T2T-CHM13v2.0.catLiftOffGenes.html \
 GCA_009914755.4_T2T-CHM13v2.0.catLiftOffGenesV1.html \
@@ -25,27 +31,70 @@
 GCA_009914755.4_T2T-CHM13v2.0.rdnaModel.html \
 GCA_009914755.4_T2T-CHM13v2.0.rnaseq.html \
 GCA_009914755.4_T2T-CHM13v2.0.sedefSegDups.html
 
 # tracks not used, and userTrackDb comes from T2T porting project
 
 notPushed = html/GCA_009914755.4_T2T-CHM13v2.0.augustus.html \
 html/GCA_009914755.4_T2T-CHM13v2.0.tanDups.html \
 trackDb/GCA_009914755.4_T2T-CHM13v2.0.userTrackDb.txt
 
 # files used to construct a useOneFile hub.txt
 hubTxt = hub/GCA_009914755.4_T2T-CHM13v2.0.hub.txt \
 hub/GCA_009914755.4_T2T-CHM13v2.0.genomes.txt \
 trackDb/GCA_009914755.4_T2T-CHM13v2.0.trackDb.txt
 
-singleFileHub: ${hubTxt}
-	@rm -f hub.txt
-	@grep -v genomesFile hub/GCA_009914755.4_T2T-CHM13v2.0.hub.txt > hub.txt
-	@printf "useOneFile on\n\n" >> hub.txt
-	@grep -v trackDb hub/GCA_009914755.4_T2T-CHM13v2.0.genomes.txt >> hub.txt
-	@echo >> hub.txt
-	@cat trackDb/GCA_009914755.4_T2T-CHM13v2.0.trackDb.txt >> hub.txt
+alpha:: singleFileHub
+	@printf "# setting up hub files for hgdownload-test staging\n"
+	make stageFiles
+	make test
+
+# 	@printf "# %s %s\n" "$*" "${stageDir}"
+
+stageFiles: $(htmlFiles:%=%stageFiles)
+%stageFiles:
+	@rm -f "${stageDir}/$*"
+	@cp --remove-destination -p "$*" "${stageDir}/$*"
+
+# verify the hub is functioning OK on hgwdev/genome-test from hgdownload-test
+# can't yet use -checkSettings with hubCheck - there are some warnings there
+# that cause this test to fail
+test:
+	@printf "# verify hub is functioning from hgdownload-test.gi.ucsc.edu\n"
+	hubCheck "https://hgdownload-test.gi.ucsc.edu/hubs/GCA/009/914/755/GCA_009914755.4/hub.txt"
+	@printf "hubCheck OK\n"
+	@printf "track count: %d tracks via API list tracks\n" "`curl -L "https://genome-test.gi.ucsc.edu/list/tracks?genome=GCA_009914755.4;trackLeavesOnly=1;hubUrl=https://hgdownload-test.gi.ucsc.edu/hubs/GCA/009/914/755/GCA_009914755.4/hub.txt"  2> /dev/null | python -mjson.tool | egrep ": {$$"  | tr -d '"' | sed -e 's/^ \+//; s/ {//;' | xargs echo | wc -w`"
+	@printf "should be more than 70 tracks\n"
+
+
+# verify the hub is functioning OK from hgdownload.soe.ucsc.edu
+verify:
+	@printf "# verify hub is functioning from hgdownload.soe.ucsc.edu\n"
+	hubCheck "https://hgdownload.soe.ucsc.edu/hubs/GCA/009/914/755/GCA_009914755.4/hub.txt"
+	@printf "hubCheck OK\n"
+	@printf "track count: %d tracks via API list tracks\n" "`curl -L "https://apibeta.soe.ucsc.edu/list/tracks?genome=GCA_009914755.4;trackLeavesOnly=1;hubUrl=https://hgdownload-test.gi.ucsc.edu/hubs/GCA/009/914/755/GCA_009914755.4/hub.txt"  2> /dev/null | python -mjson.tool | egrep ": {$$"  | tr -d '"' | sed -e 's/^ \+//; s/ {//;' | xargs echo | wc -w`"
+	@printf "should be more than 70 tracks\n"
+
+# push the hub to hgdownload
+public:
+	@printf "pushing to hgdownload\n" 1>&2
+	rsync --delete --exclude="hub.txt" --exclude="download.hub.txt" --stats -a -L -P "${pushFromDir}/" "qateam@hgdownload.soe.ucsc.edu:${pushToDir}/" 2>&1 | grep -v "X11 forwarding request" || true
+	rsync --stats -a -L -P "${pushFromDir}/download.hub.txt" "qateam@hgdownload.soe.ucsc.edu:${pushToDir}/hub.txt" 2>&1 | grep -v "X11 forwarding request" || true
+	@printf "# successful rsync\n" 1>&2
 
-alpha: singleFileHub
 
 clean::
 	rm -f hub.txt
+
+singleFileHub: ${hubTxt}
+	@rm -f hub.txt
+	@grep -v genomesFile hub/${asmId}.hub.txt > hub.txt
+	@printf "useOneFile on\n\n" >> hub.txt
+	@grep -v trackDb hub/${asmId}.genomes.txt >> hub.txt
+	@echo >> hub.txt
+	@cat trackDb/${asmId}.trackDb.txt >> hub.txt
+	@cp --remove-destination -p hub.txt ${stageDir}/${asmId}.singleFile.hub.txt
+	@cp --remove-destination -p hub.txt ${stageDir}/${asmId}.download.hub.txt
+	@cp --remove-destination -p hub/${asmId}.groups.txt ${stageDir}/
+	@cp --remove-destination -p hub/${asmId}.genomes.txt ${stageDir}/
+	cp --remove-destination -p hub/${asmId}.hub.txt ${stageDir}/
+	cp --remove-destination -p trackDb/${asmId}.trackDb.txt ${stageDir}/