88e5bf615b39ac9a8c93c140dbac9c1f5ea12885
max
  Wed Nov 26 03:07:29 2014 -0800
extending makefile refs #14393
diff --git src/beacon/makefile src/beacon/makefile
index faf274f..7b16b01 100644
--- src/beacon/makefile
+++ src/beacon/makefile
@@ -4,33 +4,53 @@
 #include ../../inc/cgi_build_rules.mk
 
 ifeq (${CGI_BIN_USER},)
     CGI_BIN_USER=${CGI_BIN}-${USER}
 endif
 
 ifeq (${CGI_BIN_BETA},)
     CGI_BIN_BETA=${CGI_BIN}-beta
 endif
 
 my::
 	pylint -E query
 	mkdir -p ${CGI_BIN_USER}/beacon
 	rm -f ${CGI_BIN_USER}/beacon/query
 	cp -p query ${CGI_BIN_USER}/beacon/
-beta::
-	pylint -E query
-	mkdir -p ${CGI_BIN_BETA}/beacon
-	rm -f ${CGI_BIN_BETA}/beacon/query
-	cp -p query ${CGI_BIN_BETA}/beacon/
+	cp -p accCounts.gdbm ${CGI_BIN_USER}/beacon/
+	chmod a+w ${CGI_BIN_USER}/beacon/accCounts.gdbm
+	cp -p insdcToUcsc.tab ${CGI_BIN_USER}/beacon/
+	cp ${BINDIR}/bigBedToBed ${CGI_BIN_USER}/beacon/
+	cp /hive/data/genomes/hg19/bed/beacon/*.bb ${CGI_BIN_USER}/beacon/
+	cd ${CGI_BIN_USER}/beacon/ && ln -sf query queryHgmd && ln -sf query queryClinvar && ln -sf query queryLovd && ln -sf query queryUniprot
+
+
 alpha::
 	pylint -E query
 	mkdir -p ${CGI_BIN}/beacon
 	rm -f ${CGI_BIN}/beacon/query
-	cp -p query ${CGI_BIN}/beacon/
+	cp -p query* ${CGI_BIN}/beacon/
+	cp -p accCounts.gdbm ${CGI_BIN}/beacon/
+	chmod a+w ${CGI_BIN_USER}/beacon/accCounts.gdbm
+	cp -p insdcToUcsc.tab ${CGI_BIN}/beacon/
+	cp ${BINDIR}/bigBedToBed ${CGI_BIN}/beacon/
+	cp /hive/data/genomes/hg19/bed/beacon/*.bb ${CGI_BIN}/beacon/
+	cd ${CGI_BIN}/beacon/ && ln -sf query queryHgmd && ln -sf query queryClinvar && ln -sf query queryLovd && ln -sf query queryUniprot
+
+beta::
+	pylint -E query
+	mkdir -p ${CGI_BIN_BETA}/beacon
+	rm -f ${CGI_BIN_BETA}/beacon/query
+	cp -p query* ${CGI_BIN_BETA}/beacon/
+	cp -p accCounts.gdbm ${CGI_BIN_BETA}/beacon/
+	chmod a+w ${CGI_BIN_USER}/beacon/accCounts.gdbm
+	cp -p insdcToUcsc.tab ${CGI_BIN_BETA}/beacon/
+	# for beta, using the stable binary from /cluster/bin
+	cp /cluster/bin/x86_64/bigBedToBed ${CGI_BIN_BETA}/beacon/
+	cp /hive/data/genomes/hg19/bed/beacon/*.bb ${CGI_BIN}/beacon/
+	cd ${CGI_BIN_BETA}/beacon/ && ln -sf query queryHgmd && ln -sf query queryClinvar && ln -sf query queryLovd && ln -sf query queryUniprot
+
 clean::
+	rm -f 
 
 compile::
 
-install::
-	mkdir -p ${DESTDIR}${CGI_BIN}/beacon
-	rm -f ${DESTDIR}${CGI_BIN}/beacon/query
-	cp -p query ${DESTDIR}${CGI_BIN}/