diff options
Diffstat (limited to 'biology/subread/files/Makefile.pkg')
| -rw-r--r-- | biology/subread/files/Makefile.pkg | 104 |
1 files changed, 104 insertions, 0 deletions
diff --git a/biology/subread/files/Makefile.pkg b/biology/subread/files/Makefile.pkg new file mode 100644 index 000000000000..2ae783e69902 --- /dev/null +++ b/biology/subread/files/Makefile.pkg @@ -0,0 +1,104 @@ + + +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} |