Makefile_TRegGA-orig

#Makefile_TRegGA
#
#Makefile to run all TRegGA workflow components with one command ...
#
#Version: September 20, 2015.
include TRegGA.config

#Usage:
#
#  make -j X -f Makefile_TRegGA >& err
#
#where X is the number of processors to be used.

#Optional clean-up:
#
#  make -f Makefile_TRegGA cleanup

#Please be careful while editing the Makefile as it is 'tab-sensitive'.
#Typical customization should only involve apppropriate editing of the variables in the next section.

##########################Variable Settings#####################################
###
CHECKONLY         = yes
NUMPROC           = SET_NUMPROC

CULTIVAR          = "SET_CULTIVAR"#  Replace "SET_CULTIVAR" with an apppropriate cultivar name; e.g., "DA GANG ZHAN" (retain quotation marks)
SYNONYM           = SET_SYNONYM#  Replace SET_SYNONYM with an appropriate space-free label; e.g., Dagangzhan (no spaces, no quotation marks)

READS_DIR         = ${TRegGA_DIR}/reads/${SYNONYM}
READS_1           = ${READS_DIR}/${SYNONYM}_1#  The quality-filtered and trimmed forward reads from Makefile_GRP step
READS_2           = ${READS_DIR}/${SYNONYM}_2#  The quality-filtered and trimmed reverse reads from Makefile_GRP step

DeNOVO_DIR        = ${TRegGA_DIR}/assembly/denovo/${SYNONYM}

REFERENCE         = SET_REFERENCE
TARGET            = SET_TARGET
FROM              = SET_FROM
TO                = SET_TO



all:	checkonlyBegin \
 	${READS_1}.fa ${READS_2}.fa \
	${DeNOVO_DIR}/${SYNONYM}-GF/${SYNONYM}-GF.gapfilled.final.fa \
	${TRegGA_DIR}/targets/${TARGET}.embl \
	${TRegGA_DIR}/assembly/rfguided/${SYNONYM}-on-${TARGET}/Makefile_rfguided_${SYNONYM}-on-${TARGET} \
	checkonlyEnd



### Check only begin:
#
checkonlyBegin:
	if [ $(CHECKONLY) = yes ]; then \
		if [ ! -e ${READS_DIR} ]; then \
			mkdir ${READS_DIR}; \
			touch ${READS_1}.fq; \
			touch ${READS_1}.fa; \
			touch ${READS_2}.fq; \
			touch ${READS_2}.fa; \
		fi; \
		if [ ! -e ${TRegGA_DIR}/targets/${TARGET}.embl ]; then \
			touch ${TRegGA_DIR}/targets/${TARGET}.embl; \
		fi; \
		if [ ! -e ${TRegGA_DIR}/targets/${TARGET}.fasta ]; then \
			touch ${TRegGA_DIR}/targets/${TARGET}.fasta; \
		fi; \
		if [ ! -e ${TRegGA_DIR}/targets/${TARGET}.gff3 ]; then \
			touch ${TRegGA_DIR}/targets/${TARGET}.gff3; \
		fi; \
		sleep 1; \
	fi

### Check only end:
#
checkonlyEnd:
	if [ $(CHECKONLY) = yes ]; then \
		if [ ! -s ${READS_1}.fq ]; then \
			\rm -rf ${READS_DIR}; \
		fi; \
		if [ ! -s ${TRegGA_DIR}/targets/${TARGET}.embl ]; then \
			\rm ${TRegGA_DIR}/targets/${TARGET}.embl; \
			\rm ${TRegGA_DIR}/targets/${TARGET}.fasta; \
			\rm ${TRegGA_DIR}/targets/${TARGET}.gff3; \
		fi; \
	fi


### Read preparation:
#
${TRegGA_DIR}/reads/0Record-${SYNONYM}:	${TRegGA_DIR}/reads/0Record-template
	cd ${TRegGA_DIR}/reads; \
	sed 0Record-template -e 's/CHECKONLY/${CHECKONLY}/; s/SET_NUMPROC/${NUMPROC}/; s/SET_CULTIVAR/${CULTIVAR}/; s/SET_SYNONYM/${SYNONYM}/;' > 0Record-${SYNONYM}; \
	chmod a+x 0Record-${SYNONYM}

${TRegGA_DIR}/reads/${SYNONYM}/%_1.fa ${TRegGA_DIR}/reads/${SYNONYM}/%_2.fa:	${TRegGA_DIR}/reads/0Record-${SYNONYM}
	cd ${TRegGA_DIR}/reads; \
	./0Record-${SYNONYM}; \
	if [ $(CHECKONLY) = yes ]; then \
		if [ ! -s ${READS_1}.fq ]; then \
			\rm 0Record-${SYNONYM}; \
		fi; \
	fi



### De novo assembly:
#
${TRegGA_DIR}/assembly/denovo/0Record-${SYNONYM}:	${TRegGA_DIR}/assembly/denovo/0Record-template
	cd ${TRegGA_DIR}/assembly/denovo; \
	sed 0Record-template -e 's/CHECKONLY/${CHECKONLY}/; s/SET_NUMPROC/${NUMPROC}/; s/SET_CULTIVAR/${CULTIVAR}/; s/SET_SYNONYM/${SYNONYM}/;' > 0Record-${SYNONYM}; \
	chmod a+x 0Record-${SYNONYM}


${DeNOVO_DIR}/${SYNONYM}-GF/${SYNONYM}-GF.gapfilled.final.fa:	${TRegGA_DIR}/assembly/denovo/0Record-${SYNONYM} ${READS_1}.fa ${READS_2}.fa
	cd ${TRegGA_DIR}/assembly/denovo; \
	./0Record-${SYNONYM}; \
	if [ $(CHECKONLY) = yes ]; then \
		if [ ! -e ${DeNOVO_DIR}/${SYNONYM}-GF/${SYNONYM}-GF.gapfilled.final.fa ]; then \
			\rm 0Record-${SYNONYM}; \
		fi; \
	fi



### Target preparation:
#
${TRegGA_DIR}/targets/0Record-${TARGET}:	${TRegGA_DIR}/targets/0Record-template
	cd ${TRegGA_DIR}/targets; \
	sed 0Record-template -e 's/CHECKONLY/${CHECKONLY}/; s/SET_REFERENCE/${REFERENCE}/; s/SET_TARGET/${TARGET}/; s/SET_FROM/${FROM}/; s/SET_TO/${TO}/;' > 0Record-${TARGET}; \
	chmod a+x 0Record-${TARGET}

${TRegGA_DIR}/targets/${TARGET}.embl:	${TRegGA_DIR}/targets/0Record-${TARGET}
	cd ${TRegGA_DIR}/targets; \
	./0Record-${TARGET}; \
	if [ $(CHECKONLY) = yes ]; then \
		if [ ! -s ${TRegGA_DIR}/targets/${TARGET}.embl ]; then \
			\rm 0Record-${TARGET}; \
		fi; \
	fi



### Reference-guided assembly:
#
${TRegGA_DIR}/assembly/rfguided/0Record-${SYNONYM}-on-${TARGET}:	${TRegGA_DIR}/assembly/rfguided/0Record-template
	cd ${TRegGA_DIR}/assembly/rfguided; \
	sed 0Record-template -e 's/CHECKONLY/${CHECKONLY}/; s/SET_NUMPROC/${NUMPROC}/; s/SET_SYNONYM/${SYNONYM}/; s/SET_TARGET/${TARGET}/; ' > 0Record-${SYNONYM}-on-${TARGET}; \
	chmod a+x 0Record-${SYNONYM}-on-${TARGET}

${TRegGA_DIR}/assembly/rfguided/${SYNONYM}-on-${TARGET}/Makefile_rfguided_${SYNONYM}-on-${TARGET}:	${TRegGA_DIR}/assembly/rfguided/0Record-${SYNONYM}-on-${TARGET} ${READS_1}.fa ${READS_2}.fa ${DeNOVO_DIR}/${SYNONYM}-GF/${SYNONYM}-GF.gapfilled.final.fa ${TRegGA_DIR}/targets/${TARGET}.embl
	cd ${TRegGA_DIR}/assembly/rfguided; \
	./0Record-${SYNONYM}-on-${TARGET}; \
	if [ $(CHECKONLY) = yes ]; then \
		if [ ! -e ${TRegGA_DIR}/assembly/rfguided/${SYNONYM}-on-${TARGET}/EVALUATION/0README ]; then \
 			\rm 0Record-${SYNONYM}-on-${TARGET}; \
		fi; \
	fi