5bf72867bf2d8aa880d82340573987b542016756
kate
  Tue Jan 27 17:26:21 2015 -0800
Add tool to check links in a table (based on columnName 'url')

diff --git src/hg/utils/makefile src/hg/utils/makefile
index a799465..aa0931d 100644
--- src/hg/utils/makefile
+++ src/hg/utils/makefile
@@ -1,101 +1,102 @@
 # Build all directories in utils
 # test comment
 # 	$Id: makefile,v 1.21 2010/06/04 00:12:42 larrym Exp $
 
 kentSrc = ../..
 
 include ${kentSrc}/inc/localEnvironment.mk
 include ${kentSrc}/inc/common.mk
 
 # to check for Mac OSX Darwin specifics:
 UNAME_S := $(shell uname -s)
 
 # can not build this on Mac OSX - has functions not supported
 ifeq ($(UNAME_S),Darwin)
   buildRefresh=
 else
   buildRefresh=refreshNamedSessionCustomTracks
 endif
 
 # List of directories to build for userApps
 UTILS_APPLIST = \
 	bedExtendRanges \
 	bedToPsl \
 	bedWeedOverlapping \
 	chromGraphFromBin \
 	chromGraphToBin \
 	crTreeIndexBed \
 	crTreeSearchBed \
 	gapToLift \
 	gff3ToGenePred \
 	gff3ToPsl \
 	gtfToGenePred \
 	hubCheck \
 	hubPublicCheck \
 	makeTableList \
 	oligoMatch \
 	overlapSelect \
 	positionalTblCheck \
 	pslMap \
 	tdbQuery \
 	twoBitMask
 
 SCRIPT_FILES = \
 	dbNsfpToBed.pl \
 	dumpDb.pl \
 	mergeOverlapBed4.pl \
 	mergeSortedBed3Plus.pl
 
 # List of directories to build of interest only at UCSC
 DIRS = ${buildRefresh} \
-	safePush \
-	toDev64 \
 	automation \
-	refSeqGet \
-	wigBedToStep \
-	pslUniq \
-	makeTrackIndex \
+	checkUrlsInTables \
 	geoMirrorNode \
-	mysqlSecurityCheck
+	makeTrackIndex \
+	mysqlSecurityCheck \
+	pslUniq \
+	refSeqGet \
+	safePush \
+	toDev64 \
+	wigBedToStep
 
 TEST_DIRS = \
 	gff3ToGenePred \
 	gff3ToPsl \
 	gtfToGenePred \
 	overlapSelect \
 	pslMap \
 	refSeqGet
 
 APPS = $(DIRS) $(UTILS_APPLIST)
 
 all:: utils
 
 utils: $(APPS:%=%.utils)
 %.utils:
 	cd $* && echo $* && $(MAKE)
 
 userApps: $(UTILS_APPLIST:%=%.userApp)
 %.userApp:
 	cd $* && echo $* && $(MAKE)
 
 scripts: $(SCRIPT_FILES:%=%.scripts)
 %.scripts:
 	chmod +x $*
 	rm -f ${SCRIPTS}/$*
 	cp -p $* ${SCRIPTS}/$*
 
 alpha: scripts all
 
 test::	${TEST_DIRS:%=%.test}
 %.test:
 	(cd $* && ${MAKE} test)
 
 clean:: $(APPS:%=%.clean)
 	- find . -name '*.o' -exec rm {} \;
 %.clean:
 	(cd $* && ${MAKE} clean)
 
 compile:: $(APPS:%=%.compile)
 	- find . -name '*.o' -exec rm {} \;
 %.compile:
 	(cd $* && ${MAKE} compile)