makefile.in

# DO NOT CHANGE

SHELL=bash
repo=$(shell pwd)
GITVERSION=$(shell git describe --tags | sed 's/^v//g')
progs = gwAlign-Extend gwAlign-Unify gwAlign_hgnc bam2consensus.py alignCDS.py
bins=$(addprefix bin/,$(progs))

### makefile core

all : $(bins)

$(bins) : bin 
	@sed -e "s/SEDMATCHGITVERSION/${GITVERSION}/g" $(subst bin/,scripts/,$@) | \
	sed -e "s/SEDMATCHPICARD/$(subst /,\\/,${PICARD})/g" | \
	sed -e "s/SEDMATCHQUEUE/${QUEUE}/g" | \
	sed -e "s/SEDMATCHMACSE/$(subst /,\\/,${MACSE})/g" > $@
	chmod 755 $@

bin :
	mkdir bin
	chmod 755 bin

.PHONY : install
install : 
	ln -s ${repo}/bin/gwAlign-Extend ${BINPATH}
	ln -s ${repo}/bin/gwAlign_hgnc ${BINPATH}
	ln -s ${repo}/bin/gwAlign-Unify ${BINPATH}
	ln -s ${repo}/bin/bam2consensus.py ${BINPATH}
	ln -s ${repo}/bin/alignCDS.py ${BINPATH}
	ln -s ${repo}/lib/gwAlign_Unify_report.rmd ${LIBPATH}

.PHONY : force_install
force_install : $(bins)
	ln -sf ${repo}/bin/gwAlign-Extend ${BINPATH}
	ln -sf ${repo}/bin/gwAlign_hgnc ${BINPATH}
	ln -sf ${repo}/bin/gwAlign-Unify ${BINPATH}
	ln -sf ${repo}/bin/bam2consensus.py ${BINPATH}
	ln -sf ${repo}/bin/alignCDS.py ${BINPATH}
	ln -sf ${repo}/lib/gwAlign_Unify_report.rmd ${LIBPATH}

.PHONY : uninstall
uninstall : 
	rm ${BINPATH}/gwAlign_hgnc
	rm ${BINPATH}/gwAlign-Extend
	rm ${BINPATH}/gwAlign-Unify
	rm ${BINPATH}/alignCDS.py
	rm ${BINPATH}/bam2consensus.py 
	
.PHONY : clean
clean :
	-rm -R bin