105 lines
3.8 KiB
Makefile
105 lines
3.8 KiB
Makefile
|
|
|
|
include makefile.version
|
|
|
|
CCFLAGS = -DMAKE_FOR_EXON -DMAKE_STANDALONE \
|
|
-DSUBREAD_VERSION=\"${SUBREAD_VERSION}\" -D_FILE_OFFSET_BITS=64
|
|
LDFLAGS += -DMAKE_FOR_EXON -DMAKE_STANDALONE -pthread -lsysinfo -lz -lm
|
|
CC ?= gcc
|
|
CC += ${CCFLAGS}
|
|
|
|
BINS = detectionCall sublong repair txUnique featureCounts removeDup \
|
|
exactSNP subread-buildindex subindel subread-align subjunc \
|
|
qualityScores subread-fullscan propmapped flattenGTF \
|
|
|
|
MKDIR ?= mkdir -p
|
|
INSTALL ?= install
|
|
DESTDIR ?= .
|
|
PREFIX ?= local
|
|
STRIP ?= strip
|
|
|
|
ALL_LIBS= core core-junction core-indel sambam-file sublog gene-algorithms hashtable input-files sorted-hashtable gene-value-index exon-algorithms HelperFunctions interval_merge long-hashtable core-bigtable seek-zlib input-blc
|
|
ALL_OBJECTS=$(addsuffix .o, ${ALL_LIBS})
|
|
ALL_H=$(addsuffix .h, ${ALL_LIBS})
|
|
ALL_C=$(addsuffix .c, ${ALL_LIBS})
|
|
|
|
all: genRandomReads detectionCall sublong repair txUnique featureCounts removeDup exactSNP subread-buildindex subindel subread-align subjunc qualityScores subread-fullscan propmapped flattenGTF # samMappedBases mergeVCF testZlib
|
|
mkdir -p ../bin/utilities
|
|
mv longread-one/LRM longread-one/sublong
|
|
mv longread-one/sublong subread-align subjunc featureCounts subindel exactSNP subread-buildindex ../bin/
|
|
mv detectionCall genRandomReads repair propmapped qualityScores removeDup subread-fullscan txUnique flattenGTF ../bin/utilities
|
|
|
|
sublong: longread-one/longread-mapping.c ${ALL_OBJECTS}
|
|
echo " " > longread-one/make.version
|
|
rm -f longread-one/*.o
|
|
cd longread-one && $(MAKE)
|
|
|
|
genRandomReads: gen_rand_reads.c ${ALL_OBJECTS}
|
|
${CC} -o genRandomReads gen_rand_reads.c ${ALL_OBJECTS} ${LDFLAGS}
|
|
|
|
flattenGTF: flattenAnnotations.c ${ALL_OBJECTS}
|
|
${CC} -o flattenGTF flattenAnnotations.c ${ALL_OBJECTS} ${LDFLAGS}
|
|
|
|
detectionCall: detection-calls.c ${ALL_OBJECTS}
|
|
${CC} -o detectionCall detection-calls.c ${ALL_OBJECTS} ${LDFLAGS}
|
|
|
|
repair: read-repair.c ${ALL_OBJECTS}
|
|
${CC} -o repair read-repair.c ${ALL_OBJECTS} ${LDFLAGS}
|
|
|
|
txUnique: tx-unique.c tx-unique.h ${ALL_OBJECTS}
|
|
${CC} -o txUnique tx-unique.c ${ALL_OBJECTS} ${LDFLAGS}
|
|
|
|
globalReassembly: global-reassembly.c ${ALL_OBJECTS}
|
|
${CC} -o globalReassembly global-reassembly.c ${ALL_OBJECTS} ${LDFLAGS}
|
|
|
|
propmapped: propmapped.c ${ALL_OBJECTS}
|
|
${CC} -o propmapped propmapped.c ${ALL_OBJECTS} ${LDFLAGS}
|
|
|
|
exactSNP: SNPCalling.c SNPCalling.h ${ALL_OBJECTS}
|
|
${CC} -o exactSNP SNPCalling.c ${ALL_OBJECTS} ${LDFLAGS}
|
|
|
|
subread-buildindex: index-builder.c subread.h ${ALL_OBJECTS}
|
|
${CC} -o subread-buildindex index-builder.c ${ALL_OBJECTS} ${LDFLAGS}
|
|
|
|
removeDup: removeDupReads.c removeDupReads.h subread.h ${ALL_OBJECTS}
|
|
${CC} -o removeDup removeDupReads.c ${ALL_OBJECTS} ${LDFLAGS}
|
|
|
|
subindel: SUBindel.c core.h subread.h ${ALL_OBJECTS}
|
|
${CC} -o subindel SUBindel.c ${ALL_OBJECTS} ${LDFLAGS}
|
|
|
|
featureCounts: readSummary.c subread.h ${ALL_OBJECTS}
|
|
${CC} -o featureCounts readSummary.c ${ALL_OBJECTS} ${LDFLAGS}
|
|
|
|
subread-align: core-interface-aligner.c ${ALL_OBJECTS}
|
|
${CC} -o subread-align core-interface-aligner.c ${ALL_OBJECTS} ${LDFLAGS}
|
|
|
|
subjunc: core-interface-subjunc.c ${ALL_OBJECTS}
|
|
${CC} -o subjunc core-interface-subjunc.c ${ALL_OBJECTS} ${LDFLAGS}
|
|
|
|
subtools: subtools.c ${ALL_OBJECTS}
|
|
${CC} -o subtools subtools.c ${ALL_OBJECTS} ${LDFLAGS}
|
|
|
|
qualityScores: qualityScores.c ${ALL_OBJECTS}
|
|
${CC} -o qualityScores qualityScores.c ${ALL_OBJECTS} ${LDFLAGS}
|
|
|
|
subread-fullscan: fullscan.c ${ALL_OBJECTS}
|
|
${CC} -o subread-fullscan fullscan.c ${ALL_OBJECTS} ${LDFLAGS}
|
|
|
|
.PHONY: clean install install-strip
|
|
|
|
install-strip: install
|
|
${STRIP} ${DESTDIR}${PREFIX}/bin/*
|
|
|
|
install:
|
|
${MKDIR} ${DESTDIR}${PREFIX}/bin
|
|
${INSTALL} -c \
|
|
../bin/exactSNP \
|
|
../bin/featureCounts \
|
|
../bin/sub* \
|
|
../bin/utilities/* \
|
|
${DESTDIR}${PREFIX}/bin
|
|
|
|
clean:
|
|
rm -f core featureCounts exactSNP removeDup subread-buildindex \
|
|
${ALL_OBJECTS}
|