b39e695f387a5f9d2d411064a13d6d0cb5991c9f
Merge parents 0f8c686fd41 386b50e1093
markd
  Thu May 1 23:08:49 2025 -0700
fixed merge conflict

diff --cc src/makefile
index 4ebb6bf0be0,7543c906c35..acc26cc8272
--- src/makefile
+++ src/makefile
@@@ -1,202 -1,201 +1,202 @@@
  include inc/localEnvironment.mk
  include inc/common.mk
  
  all: utils cgi blatSuite
  
  alpha: check-alpha clean
  	${MAKE} utils-alpha cgi-alpha blatSuite
  
 -beta: check-beta clean cgi-beta
 +beta: check-beta clean
 +	${MAKE} cgi-beta
  
  # do a git update and clean
  update:
 -	git pull
 +	${GIT} pull
  	${MAKE} clean
  ##
  # topLibs
  ##
  TOP_LIBS = lib parasol/lib htslib
  ifneq ($(wildcard jkOwnLib/*),)
    TOP_LIBS += jkOwnLib
  endif
  topLibs: topChecks | ${TOP_LIBS:%=%.topLibs}
  %.topLibs:
  	${MAKE} -C $*
  
  topChecks:
  	@./checkUmask.sh
  	@MACHTYPE=${MACHTYPE} ./machTest.sh
  
  optLib:
  	cd optimalLeaf && ${MAKE}
  
  ##
  # hgLib
  ##
  ifneq ($(wildcard hg/makefile),)
     HGLIB_DIRS += hg/lib
     HGLIB_CHECK = hgLibChecks
  endif
  ifneq ($(wildcard hg/cgilib/makefile),)
     HGLIB_DIRS += hg/cgilib
  endif
  
  hgLib: ${HGLIB_CHECK} | ${HGLIB_DIRS:%=%.hgLib}
  %.hgLib:
  	${MAKE} -C $*
  hgLibChecks:
  	@./hg/sqlEnvTest.sh
  
  libs: topLibs hgLib optLib
  
  cgi: libs
  	cd hg && ${MAKE} cgi
  	cd utils/bedToBigBed && ${MAKE} cgi
  
  cgi-alpha: check-alpha libs logUser
  	cd hg && ${MAKE} alpha
  	cd utils/bedToBigBed && ${MAKE} alpha
  
  cgi-beta: check-beta libs logUser
  	cd hg && ${MAKE} beta
  	cd utils/bedToBigBed && ${MAKE} beta
  
  # This log file can be useful when debugging problems on the alpha and beta builds.
  logUser:
  ifeq (${IS_HGWDEV},yes)
  	echo ${USER}, $(MAKECMDGOALS), `date` >> ${CGI_BIN}/buildLog.txt
  endif
  
  check-alpha:
- 	# this will fail if we are not on master branch:
- 	${GIT} branch | egrep '\* master' > /dev/null
+ 	# this will fail if we are not on master or beta branch:
 -	git branch | egrep '\* master|beta' > /dev/null
++	${GIT} branch | egrep '\* master|beta' > /dev/null
  
  check-beta:
  	# this will fail if we are not in a beta checkout:
 -	git branch | egrep '\* v[0-9]+_branch' > /dev/null	
 +	${GIT} branch | egrep '\* v[0-9]+_branch' > /dev/null	
  
  BLAT_SUITE_DIRS = blat gfClient gfServer webBlat hg/pslPretty hg/pslReps \
  	hg/pslSort utils/nibFrag utils/faToNib utils/faToTwoBit utils/twoBitToFa \
  	utils/twoBitInfo isPcr blatz
  
  blatSuite: ${BLAT_SUITE_DIRS:%=%.blatSuite}
  
  %.blatSuite: topLibs hgLib
  	 ${MAKE} -C $*
  
  # all of these application makefiles have been updated to include use
  #	of DESTDIR and BINDIR
  
  # common subdirs uses by multiple targets
  STD_DIRS = ameme index dnaDust protDust weblet aladdin primeMate fuse meta tagStorm \
  	tabFile parasol blat
  
  USER_APP_DIRS = utils parasol hg hg/utils \
  	hg/makeDb tabFile
  ALMOST_USER_APP_DIRS = blat gfClient gfServer isPcr ameme index/ixIxx utils/userApps
  
  userApps: ${USER_APP_DIRS:%=%.userApps} ${ALMOST_USER_APP_DIRS:%=%.almostUserApps}
  
  %.userApps: topLibs hgLib destBin
  	${MAKE} -C $* userApps
  
  # these dont have userApps targets
  %.almostUserApps: topLibs hgLib destBin
  	${MAKE} -C $*
  
  destBin:
  	${MKDIR} ${DESTBINDIR}
  
  CLEAN_DIRS = ${STD_DIRS} lib hg jkOwnLib htslib utils webBat isPcr
  
  clean: ${CLEAN_DIRS:%=%.clean}
  	find . -name \*.o -print | xargs --no-run-if-empty rm
  	rm -f tags TAGS
  	rm -f cscope.out cscope.files cscope.po.out
  
  %.clean:
  	if [ -e "$*/makefile" ] ; then ${MAKE} -C $* clean ; fi
  
  
  TEST_DIRS = blat gfServer hg lib utils
  test:: $(TEST_DIRS:%=%.test)
  %.test:
  	if test -d $* ; then ${MAKE} -C $* test; fi
  
  LIB_TAGS_IN = lib/*.[hc] */lib/*.[hc] */*/lib/*.[hc] */*/*/lib/*.[hc] jkOwnLib/*.c \
  	inc/*.h */inc/*.h */*/inc/*.h */*/*/inc/*.h */cgilib/*.[hc]
  
  # build tags for libraries
  .PHONY: tags
  tags:
  	ctags ${LIB_TAGS_IN}
  
  cscope.out:
  	find `pwd` -name '*.c' -o -name '*.h' > cscope.files
  	cscope -qRb `cat cscope.files`
  search: cscope.out
  	cscope -d
  
  # build emacs tags for libraries
  .PHONY: etags
  etags:
  	etags ${LIB_TAGS_IN}
  
  # build tags for all files
  .PHONY: tags-all
  tags-all:
  	find . -name '*.[ch]' | grep -v "/userApps/" | ctags -L -
  
  # build emacs tags for all files
  .PHONY: etags-all
  etags-all:
  	find . -name '*.[ch]' | etags -
  
  UTILS_DIRS = ${DIRS} utils
  .PHONY: utils
  utils: ${UTILS_DIRS:%=%.utils} ${STD_DIRS:%=%.utils}
  
  %.utils: libs destBin hgutils
  	@${MKDIR} ${SCRIPTS}
  	${MAKE} -C $*
  
  utils-alpha: ${UTILS_DIRS:%=%.utils-alpha}
  
  %.utils-alpha: check-alpha libs destBin hgutils
  	if [ -e "$*/makefile" ] ; then ${MAKE} -C $* ; fi
  
  hgutils: libs destBin
  	cd hg && ${MAKE} utils
  
  ##  cellar archive for obsolete programs
  
  cellarDirs = cdnaAli getgene idbQuery reformat scanIntrons tracks wormAli \
  	xenoAli
  
  buildCellar: $(cellarDirs:%=%.cellar)
  
  %.cellar: libs destBin
  	cd $* && echo $* && $(MAKE)
  
  cleanCellar: $(cellarDirs:%=%.cellarClean)
  %.cellarClean:
  	cd $* && echo $* && $(MAKE) clean
  
  ## top level target for everything html related
  DOCS_LIST = hg/htdocs hg/js hg/htdocs/style
  doc: ${DOCS_LIST:%=%.docuser}
  %.docuser:
  	cd $* && $(MAKE)
  
  doc-alpha: ${DOCS_LIST:%=%.docalpha}
  %.docalpha:
  	cd $* && $(MAKE) alpha
  
  doc-beta: ${DOCS_LIST:%=%.docbeta}
  %.docbeta:
  	cd $* && $(MAKE) beta
  
  doc-install: ${DOCS_LIST:%=%.docinstall}
  %.docinstall:
  	cd $* && $(MAKE) install