a3a313b3fa4aa9c77d0b9827f8721ef57990bebd
hiram
  Tue Jan 14 12:24:02 2025 -0800
no using kmerPrint.py in place of kmerPrint.pl no redmine

diff --git src/hg/utils/automation/makefile src/hg/utils/automation/makefile
index bd81a53..0667235 100644
--- src/hg/utils/automation/makefile
+++ src/hg/utils/automation/makefile
@@ -1,106 +1,109 @@
 kentSrc = ../../..
 # Build all directories in utils
 
 include ../../../inc/common.mk
 
 PIPE_LIB = \
 	Encode.pm \
 	HgAutomate.pm \
 	HgDb.pm \
 	RAFile.pm \
 	SafePipe.pm
 
 LIB_FILES = \
 	${PIPE_LIB} \
 	EnsGeneAutomate.pm \
 	HgRemoteScript.pm \
 	HgStepManager.pm \
 	AsmHub.pm
 
 SCRIPT_FILES = \
 	asmHubAllGaps.pl \
 	asmHubAssembly.pl \
 	asmHubAugustusGene.pl \
 	asmHubCpG.pl \
 	asmHubEnsGene.pl \
 	asmHubGap.pl \
 	asmHubGatewayPage.pl \
 	asmHubGc5Percent.pl \
 	asmHubHtml.pl \
 	asmHubRepeatMasker.sh \
 	asmHubRmsk.pl \
+	asmHubRmskJoinAlign.pl \
 	asmHubSimpleRepeat.pl \
 	asmHubTrackDb.sh \
 	asmHubWindowMasker.pl \
 	blastz-make-joblist \
 	blastz-normalizeLav \
 	blastz-run-ucsc \
 	doAssemblyHub.pl \
 	doAugustus.pl \
 	doBlastzChainNet.pl \
 	doCpgIslands.pl \
 	doEnsGeneUpdate.pl \
 	doGenscan.pl \
 	doHgNearBlastp.pl \
 	doIdKeys.pl \
 	ensemblInfo.pl \
 	synBlastp.csh \
 	doRecipBest.pl \
 	doRepeatMasker.pl \
+	doRepeatModeler.pl \
 	doWindowMasker.pl \
 	doSimpleRepeat.pl \
 	doSameSpeciesLiftOver.pl \
 	ensVersions \
 	extractNestedRepeats.pl \
 	extractGtf.pl \
 	kmerPairs.pl \
 	kmerCollapsePairedEnds.pl \
 	kmerPrint.pl \
+	kmerPrint.py \
 	liftRMAlign.pl \
 	makeDownloads.pl \
 	makeGenomeDb.pl \
 	makePushQSql.pl \
 	monthlyUpdateIgtc.csh \
 	simplePartition.pl \
 	partitionSequence.pl \
 	updateIgtc.pl \
 	unigene.csh
 
 all: mkDir libFiles $(SCRIPT_FILES:%=%.all)
 
 %.all:
 	rm -f ${SCRIPTS}/$*
 	echo cp -p $* ${SCRIPTS}
 	cp -p $* ${SCRIPTS}
 	chmod +x ${SCRIPTS}/$*
 
 mkDir:
 	${MKDIR} ${SCRIPTS}
 
 libFiles: mkDir $(LIB_FILES:%=%.libFile)
 
 %.libFile:
 	rm -f ${SCRIPTS}/$*
 	echo cp -p $* ${SCRIPTS}
 	cp -p $* ${SCRIPTS}
 	chmod 664 ${SCRIPTS}/$*
 
 alpha: all
 
 development:
 	@${MAKE} --no-print-directory SCRIPTS=${PIPELINE_PATH}/encpipeline_${USER}/bin/scripts pipelibs
 
 beta:
 	@${MAKE} --no-print-directory SCRIPTS=${PIPELINE_PATH}/encpipeline_beta/bin/scripts pipelibs 
 
 prod:
 	@${MAKE} --no-print-directory SCRIPTS=${PIPELINE_PATH}/encpipeline_prod/bin/scripts pipelibs 
 
 pipelibs: ${PIPE_LIB:%=${SCRIPTS}/%}
 
 ${SCRIPTS}/% : %
 	perl -c $< 2>&1
 	cp -p $< $@.tmp
 	mv -f $@.tmp $@
 clean:
 	@echo nothing to clean in src/hg/utils/automation/