X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=makefile;h=3c48e69e91f6dbefee50b52d5d3a14b08dcac4ec;hb=dbcf1cfb8ad1086c21d64e249f012809403e7ddc;hp=c9f37a8279701589aae3b593874dab5e399bc256;hpb=4496388fd52d4354c746f36b1998477f31c2b0dd;p=rsem.git

diff --git a/makefile b/makefile
index c9f37a8..3c48e69 100644
--- a/makefile
+++ b/makefile
@@ -1,8 +1,7 @@
 CC = g++
 CFLAGS = -Wall -c -I.
 COFLAGS = -Wall -O3 -ffast-math -c -I.
-PROGRAMS = rsem-extract-reference-transcripts rsem-synthesis-reference-transcripts rsem-preref rsem-parse-alignments rsem-build-read-index rsem-run-em rsem-tbam2gbam rsem-run-gibbs rsem-calculate-credibility-intervals rsem-simulate-reads rsem-bam2wig rsem-get-unique rsem-bam2readdepth rsem-sam-validator rsem-scan-for-paired-end-reads rsem-for-ebseq-calculate-clustering-info
-
+PROGRAMS = rsem-extract-reference-transcripts rsem-synthesis-reference-transcripts rsem-preref rsem-parse-alignments rsem-build-read-index rsem-run-em rsem-tbam2gbam rsem-run-gibbs rsem-calculate-credibility-intervals rsem-simulate-reads rsem-bam2wig rsem-get-unique rsem-bam2readdepth rsem-sam-validator rsem-scan-for-paired-end-reads
 
 all : $(PROGRAMS)
 
@@ -96,10 +95,10 @@ BamConverter.h : utils.h my_assert.h sam/sam.h sam/bam.h sam_rsem_aux.h sam_rsem
 rsem-tbam2gbam : utils.h Transcripts.h Transcript.h bc_aux.h BamConverter.h sam/sam.h sam/bam.h sam/libbam.a sam_rsem_aux.h sam_rsem_cvt.h tbam2gbam.cpp sam/libbam.a
 	$(CC) -O3 -Wall tbam2gbam.cpp sam/libbam.a -lz -o $@
 
-rsem-bam2wig : wiggle.h wiggle.o sam/libbam.a bam2wig.cpp
+rsem-bam2wig : utils.h my_assert.h wiggle.h wiggle.o sam/libbam.a bam2wig.cpp
 	$(CC) -O3 -Wall bam2wig.cpp wiggle.o sam/libbam.a -lz -o $@
 
-rsem-bam2readdepth : wiggle.h wiggle.o sam/libbam.a bam2readdepth.cpp
+rsem-bam2readdepth : utils.h my_assert.h wiggle.h wiggle.o sam/libbam.a bam2readdepth.cpp
 	$(CC) -O3 -Wall bam2readdepth.cpp wiggle.o sam/libbam.a -lz -o $@
 
 wiggle.o: sam/bam.h sam/sam.h wiggle.cpp wiggle.h
@@ -136,10 +135,12 @@ rsem-sam-validator : sam/bam.h sam/sam.h my_assert.h samValidator.cpp sam/libbam
 rsem-scan-for-paired-end-reads : sam/bam.h sam/sam.h my_assert.h scanForPairedEndReads.cpp sam/libbam.a
 	$(CC) -O3 -Wall scanForPairedEndReads.cpp sam/libbam.a -lz -o $@
 
-rsem-for-ebseq-calculate-clustering-info : calcClusteringInfo.cpp
-	$(CC) -O3 -Wall calcClusteringInfo.cpp -o $@
+.PHONY: ebseq
+
+ebseq :
+	cd EBSeq ; ${MAKE} all
 
-clean:
+clean :
 	rm -f *.o *~ $(PROGRAMS)
 	cd sam ; ${MAKE} clean
-
+	cd EBSeq ; ${MAKE} clean