X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=makefile;h=97cba95d1e8aad570e1f40d871f2c80b8a054768;hb=90df7a1408511063de96e29658ffa289d43cc0bb;hp=df8d2a1c1605592b1e3cf4b346458b9b3529c22b;hpb=58f823f5be6dfbe00896fc44ac3aac5e881e9c5c;p=rsem.git

diff --git a/makefile b/makefile
index df8d2a1..97cba95 100644
--- a/makefile
+++ b/makefile
@@ -48,13 +48,13 @@ PairedEndHit.h : SingleHit.h
 HitContainer.h : GroupInfo.h
 
 
-SamParser.h : sam/sam.h sam/bam.h utils.h SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h SingleHit.h PairedEndHit.h Transcript.h Transcripts.h
+SamParser.h : sam/sam.h sam/bam.h utils.h SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h SingleHit.h PairedEndHit.h RefSeq.h Refs.h
 
 
 rsem-parse-alignments : parseIt.o sam/libbam.a
 	$(CC) -o rsem-parse-alignments parseIt.o sam/libbam.a -lz 
 
-parseIt.o : utils.h GroupInfo.h Read.h SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h SingleHit.h PairedEndHit.h HitContainer.h SamParser.h Transcript.h Transcripts.h sam/sam.h sam/bam.h parseIt.cpp
+parseIt.o : utils.h GroupInfo.h Read.h SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h SingleHit.h PairedEndHit.h HitContainer.h SamParser.h RefSeq.h Refs.h sam/sam.h sam/bam.h parseIt.cpp
 	$(CC) $(COFLAGS) parseIt.cpp
 
 
@@ -92,7 +92,7 @@ simulation.o : utils.h Read.h SingleRead.h SingleReadQ.h PairedEndRead.h PairedE
 	$(CC) $(COFLAGS) simulation.cpp
 
 rsem-run-gibbs : Gibbs.o
-	$(CC) -o rsem-run-gibbs Gibbs.o 
+	$(CC) -o rsem-run-gibbs Gibbs.o -lpthread
 
 #some header files are omitted
 Gibbs.o : utils.h Model.h SingleModel.h SingleQModel.h PairedEndModel.h PairedEndQModel.h RefSeq.h RefSeqPolicy.h PolyARules.h Refs.h GroupInfo.h boost/random.hpp Gibbs.cpp 
@@ -102,7 +102,7 @@ rsem-calculate-credibility-intervals : calcCI.o
 	$(CC) -o rsem-calculate-credibility-intervals calcCI.o
 
 #some header files are omitted
-calcCI.o : utils.h Model.h SingleModel.h SingleQModel.h PairedEndModel.h PairedEndQModel.h RefSeq.h RefSeqPolicy.h PolyARules.h Refs.h GroupInfo.h calcCI.cpp
+calcCI.o : utils.h Model.h SingleModel.h SingleQModel.h PairedEndModel.h PairedEndQModel.h RefSeq.h RefSeqPolicy.h PolyARules.h Refs.h GroupInfo.h calcCI.cpp boost/random.hpp
 	$(CC) $(COFLAGS) calcCI.cpp
 
 clean: