userApps working as before on hgwdev

ucscGenomeBrowser · Jan 29, 2025 · 4d1132f · 4d1132f
1 parent 0763964
commit 4d1132f
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Showing 9 changed files with 35 additions and 156 deletions.
diff --git a/src/ameme/makefile b/src/ameme/makefile
@@ -1,4 +1,5 @@
 kentSrc = ..
 A = ameme
 extraObjects = fragFind.o
+extraHeaders = fragFind.h
 include $(kentSrc)/inc/userApp.mk
diff --git a/src/hg/makeDb/hgGoldGapGl/makefile b/src/hg/makeDb/hgGoldGapGl/makefile
@@ -1,3 +1,5 @@
 kentSrc = ../../..
-A = hgLoadGap
+A = hgGoldGapGl hgLoadGap
+extraHeaders = ntContig.h
+extraObjects = ntContig.o
 include ${kentSrc}/inc/userApp.mk
diff --git a/src/hg/makeDb/hgLoadWiggle/makefile b/src/hg/makeDb/hgLoadWiggle/makefile
@@ -1,27 +1,17 @@
 kentSrc = ../../..
 A = hgLoadWiggle hgWiggle wigEncode
-
-include ${kentSrc}/inc/userApp.mk
+include ${kentSrc}/inc/cgiLoader.mk
 
 perl_progs = fixStepToBedGraph varStepToBedGraph
-default:: ${perl_progs:%=%.pl}
+default:: ${perl_progs:%=${DESTDIR}${BINDIR}/%.pl}
+
+${DESTDIR}${BINDIR}/%.pl: %.pl
+	@mkdir -p $(dir $@)
+	cp -f $< $@
 
 clean::
 	rm -f test_data/chr1_0.wib test_data/chr1_0.wig test_data/chr1_1.wib \
 	test_data/chr1_1.wig test_data/chr1_2.wib test_data/chr1_2.wig \
 	test_data/chr1_begin.ascii test_data/chr1_end.ascii \
 	test_data/chr1_middle.ascii test_data/chrM.ascii test_data/chrM.wib \
 	test_data/chrM.wig test_data/wiggle.tab
-
-user_loader_dir = ${CGI_BIN}-${USER}/loader
-alpha_loader_dir = ${CGI_BIN}/loader
-beta_loader_dir = ${CGI_BIN}-beta/loader
-
-cgi:: ${A:%=${user_loader_dir}/%}
-
-${user_loader_dir}/%: %
-	@{MKDIR} $(dir $@)
-	cp -f $< $@
-
-alpha:: 
-
diff --git a/src/hg/utils/chainToBigChain/makefile b/src/hg/utils/chainToBigChain/makefile
@@ -1,54 +1,4 @@
 COPT=-ggdb
 kentSrc = ../../..
 A = chainToBigChain
-include $(kentSrc)/inc/userApp.mk
-
-cgi:: compile
-	chmod a+rx $A${EXE}
-	@if [ ! -d "${CGI_BIN}-${USER}/loader" ]; then \
-		${MKDIR} ${CGI_BIN}-${USER}/loader; \
-	fi
-	rm -f ${CGI_BIN}-${USER}/loader/$A
-	mv $A${EXE} ${CGI_BIN}-${USER}/loader/$A
-	for F in ${SQL_FILES}; do \
-	    B=`basename $$F` ; \
-	    rm -f ${DESTDIR}${CGI_BIN}-${USER}/loader/$$B ; \
-	    cp -p $$F ${DESTDIR}${CGI_BIN}-${USER}/loader/$$B ; \
-	done
-
-alpha:: strip
-	@if [ ! -d "${CGI_BIN}/loader" ]; then \
-		${MKDIR} ${CGI_BIN}/loader; \
-	fi
-	rm -f ${CGI_BIN}/loader/$A
-	mv $A${EXE} ${CGI_BIN}/loader/$A
-	for F in ${SQL_FILES}; do \
-	    B=`basename $$F` ; \
-	    rm -f ${DESTDIR}${CGI_BIN}/loader/$$B ; \
-	    cp -p $$F ${DESTDIR}${CGI_BIN}/loader/$$B ; \
-	done
-
-beta:: strip
-	@if [ ! -d "${CGI_BIN}-beta/loader" ]; then \
-		${MKDIR} ${CGI_BIN}-beta/loader; \
-	fi
-	rm -f ${CGI_BIN}-beta/loader/$A
-	mv $A${EXE} ${CGI_BIN}-beta/loader/$A
-	for F in ${SQL_FILES}; do \
-	    B=`basename $$F` ; \
-	    rm -f ${DESTDIR}${CGI_BIN}-beta/loader/$$B ; \
-	    cp -p $$F ${DESTDIR}${CGI_BIN}-beta/loader/$$B ; \
-	done
-
-strip::  compile
-	${STRIP} $A${EXE}
-	chmod g+w $A${EXE}
-	chmod a+rx $A${EXE}
-
-debug:: $O
-	${CC} $O ${MYLIBS} ${L}
-	mv ${AOUT} $A${EXE}
-
-clean::
-	rm -f $O $A${EXE} tests/bed.tab
-
+include ${kentSrc}/inc/cgiLoader.mk
diff --git a/src/hg/utils/overlapSelect/makefile b/src/hg/utils/overlapSelect/makefile
@@ -1,7 +1,7 @@
 kentSrc = ../../..
 A = overlapSelect
 extraHeaders = rowReader.h chromAnn.h chromAnnMap.h selectTable.h coordCols.h \
-	usage.h 
+	usage.h
 extraObjects = rowReader.o chromAnn.o chromAnnMap.o selectTable.o coordCols.o
 include ${kentSrc}/inc/userApp.mk
 

diff --git a/src/inc/cgiLoader.mk b/src/inc/cgiLoader.mk
@@ -15,28 +15,13 @@ cgi:: compile
 	chmod a+rx ${A:%=%${EXE}}
 	${MKDIR} ${CGI_BIN}-${USER}/loader; \
 	mv -f ${A:%=%${EXE}} ${CGI_BIN}-${USER}/loader/
-	for F in ${SQL_FILES}; do \
-	    B=`basename $$F` ; \
-	    rm -f ${DESTDIR}${CGI_BIN}-${USER}/loader/$$B ; \
-	    cp -p $$F ${DESTDIR}${CGI_BIN}-${USER}/loader/$$B ; \
-	done
 
-alpha:: strip
+alpha:: compile
 	${MKDIR} ${CGI_BIN}/loader; \
-	mv -f ${A:%=%${EXE}} ${CGI_BIN}/loader/
-	for F in ${SQL_FILES}; do \
-	    B=`basename $$F` ; \
-	    rm -f ${DESTDIR}${CGI_BIN}/loader/$$B ; \
-	    cp -p $$F ${DESTDIR}${CGI_BIN}/loader/$$B ; \
-	done
+	${STRIP} ${A:%=%${EXE}}
+	cp -f ${A:%=%${EXE}} ${CGI_BIN}/loader/
 
-beta:: strip
+beta:: compile
 	${MKDIR} ${CGI_BIN}-beta/loader; \
-	mv -f ${A:%=%${EXE}} ${CGI_BIN}-beta/loader/
-	for F in ${SQL_FILES}; do \
-	    B=`basename $$F` ; \
-	    rm -f ${DESTDIR}${CGI_BIN}-beta/loader/$$B ; \
-	    cp -p $$F ${DESTDIR}${CGI_BIN}-beta/loader/$$B ; \
-	done
-
-
+	${STRIP} ${A:%=%${EXE}}
+	cp -f ${A:%=%${EXE}} ${CGI_BIN}-beta/loader/
diff --git a/src/inc/common.mk b/src/inc/common.mk
@@ -3,6 +3,13 @@ CC?=gcc
 # allow the somewhat more modern C syntax, e.g. 'for (int i=5; i<10, i++)'
 CFLAGS += -std=c99
 
+# This is required to get the cgiLoader.mk compile target to work.  for some
+# reason, make's %.o: %.c overrides the rule below, cause the compiles to fail
+# due to lack of -I flags in rule.  Running with make -r to not use built-in
+# rules fixes, however MAKEFLAGS += -r doesn't do the trick, this does.
+# make is a very mysterious fellow traveler.
+GNUMAKEFLAGS += -r
+
 # add additional library paths
 L += ${LDFLAGS}
 
@@ -25,6 +32,8 @@ HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../i
 
 # to check for Mac OSX Darwin specifics:
 UNAME_S := $(shell uname -s)
+# to check for differences in Linux OS version
+KERNEL_REL := $(shell uname -r)
 # to check for builds on hgwdev
 HOSTNAME = $(shell uname -n)
 
@@ -169,6 +178,10 @@ endif
 
 ifneq ($(UNAME_S),Darwin)
   L+=${PTHREADLIB}
+  ifneq ($(filter 3.%, ${KERNEL_REL}),)
+     # older linux needed libconv
+    XXXICONVLIB=-liconv
+  endif
 else
   ifeq (${ICONVLIB},)
     ICONVLIB=-liconv
@@ -476,7 +489,6 @@ PIPELINE_PATH=/hive/groups/encode/dcc/pipeline
 CONFIG_DIR = ${PIPELINE_PATH}/${PIPELINE_DIR}/config
 ENCODEDCC_DIR = ${PIPELINE_PATH}/downloads/encodeDCC
 
-
 CC_PROG_OPTS = ${COPT} ${CFLAGS} ${HG_DEFS} ${LOWELAB_DEFS} ${HG_WARN} ${HG_INC} ${XINC}
 %.o: %.c
 	${CC} ${CC_PROG_OPTS} -o $@ -c $<

diff --git a/src/inc/userApp.mk b/src/inc/userApp.mk
@@ -35,7 +35,9 @@ objects = ${extraObjects} ${externObjects}
 
 default:: ${A:%=${DESTDIR}${BINDIR}/%${EXE}}
 
-${DESTDIR}${BINDIR}/%${EXE}: ${DEPLIBS} %.o ${objects}
+${extraObjects}: ${extraHeaders}
+
+${DESTDIR}${BINDIR}/%${EXE}: %.o ${objects} ${DEPLIBS}
 	@mkdir -p $(dir $@)
 	${CC} ${COPT} -o $@ $*.o ${objects} ${LINKLIBS} ${L}
 	${STRIP} ${DESTDIR}${BINDIR}/${A}${EXE}

diff --git a/src/utils/bedToBigBed/makefile b/src/utils/bedToBigBed/makefile
@@ -1,66 +1,3 @@
 kentSrc = ../..
 A = bedToBigBed
-include $(kentSrc)/inc/userApp.mk
-L += ${SOCKETLIB}
-
-cgi:: compile
-	chmod a+rx $A${EXE}
-	@if [ ! -d "${CGI_BIN}-${USER}/loader" ]; then \
-		${MKDIR} ${CGI_BIN}-${USER}/loader; \
-	fi
-	rm -f ${CGI_BIN}-${USER}/loader/$A
-	mv $A${EXE} ${CGI_BIN}-${USER}/loader/$A
-	for F in ${SQL_FILES}; do \
-	    B=`basename $$F` ; \
-	    rm -f ${DESTDIR}${CGI_BIN}-${USER}/loader/$$B ; \
-	    cp -p $$F ${DESTDIR}${CGI_BIN}-${USER}/loader/$$B ; \
-	done
-
-alpha:: strip
-	@if [ ! -d "${CGI_BIN}/loader" ]; then \
-		${MKDIR} ${CGI_BIN}/loader; \
-	fi
-	rm -f ${CGI_BIN}/loader/$A
-	mv $A${EXE} ${CGI_BIN}/loader/$A
-	for F in ${SQL_FILES}; do \
-	    B=`basename $$F` ; \
-	    rm -f ${DESTDIR}${CGI_BIN}/loader/$$B ; \
-	    cp -p $$F ${DESTDIR}${CGI_BIN}/loader/$$B ; \
-	done
-
-beta:: strip
-	@if [ ! -d "${CGI_BIN}-beta/loader" ]; then \
-		${MKDIR} ${CGI_BIN}-beta/loader; \
-	fi
-	rm -f ${CGI_BIN}-beta/loader/$A
-	mv $A${EXE} ${CGI_BIN}-beta/loader/$A
-	for F in ${SQL_FILES}; do \
-	    B=`basename $$F` ; \
-	    rm -f ${DESTDIR}${CGI_BIN}-beta/loader/$$B ; \
-	    cp -p $$F ${DESTDIR}${CGI_BIN}-beta/loader/$$B ; \
-	done
-
-strip::  compile
-	${STRIP} $A${EXE}
-	chmod g+w $A${EXE}
-	chmod a+rx $A${EXE}
-
-install::  strip
-	@if [ ! -d "${DESTDIR}${CGI_BIN}/loader" ]; then \
-		${MKDIR} "${DESTDIR}${CGI_BIN}/loader"; \
-	fi
-	rm -f ${DESTDIR}${CGI_BIN}/loader/$A
-	mv $A${EXE} ${DESTDIR}${CGI_BIN}/loader/$A
-	for F in ${SQL_FILES}; do \
-	    B=`basename $$F` ; \
-	    rm -f ${DESTDIR}${CGI_BIN}/loader/$$B ; \
-	    cp -p $$F ${DESTDIR}${CGI_BIN}/loader/$$B ; \
-	done
-
-debug:: $O
-	${CC} $O ${MYLIBS} ${L}
-	mv ${AOUT} $A${EXE}
-
-clean::
-	rm -f $O $A${EXE} tests/bed.tab
-
+include ${kentSrc}/inc/cgiLoader.mk