Description: use Debian's boost library
Author: Michael R. Crusoe <crusoe@ucdavis.edu>
--- rsem.orig/Makefile
+++ rsem/Makefile
@@ -1,6 +1,6 @@
 CC = g++
-CFLAGS = -Wall -c -I.
-COFLAGS = -Wall -O3 -ffast-math -c -I.
+CFLAGS = -Wall -c -I. -I/usr/include/
+COFLAGS = -Wall -O3 -ffast-math -c -I. -I/usr/include
 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
 
 .PHONY : all ebseq clean
@@ -59,8 +59,6 @@
 	$(CC) -O3 buildReadIndex.cpp -o rsem-build-read-index
 
 
-simul.h : boost/random.hpp
-
 ReadReader.h : SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h ReadIndex.h
 
 SingleModel.h : utils.h my_assert.h Orientation.h LenDist.h RSPD.h Profile.h NoiseProfile.h ModelParams.h RefSeq.h Refs.h SingleRead.h SingleHit.h ReadReader.h simul.h
@@ -77,14 +75,12 @@
 
 BamWriter.h : sam_rsem_aux.h sam_rsem_cvt.h SingleHit.h PairedEndHit.h HitWrapper.h Transcript.h Transcripts.h
 
-sampling.h : boost/random.hpp
-
 WriteResults.h : utils.h my_assert.h GroupInfo.h Transcript.h Transcripts.h RefSeq.h Refs.h Model.h SingleModel.h SingleQModel.h PairedEndModel.h PairedEndQModel.h
 
 rsem-run-em : EM.o
 	$(CC) -o rsem-run-em EM.o /usr/lib/libbam.a -lz -lpthread
 
-EM.o : utils.h my_assert.h Read.h SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h SingleHit.h PairedEndHit.h Model.h SingleModel.h SingleQModel.h PairedEndModel.h PairedEndQModel.h Refs.h GroupInfo.h HitContainer.h ReadIndex.h ReadReader.h Orientation.h LenDist.h RSPD.h QualDist.h QProfile.h NoiseQProfile.h ModelParams.h RefSeq.h RefSeqPolicy.h PolyARules.h Profile.h NoiseProfile.h Transcript.h Transcripts.h HitWrapper.h BamWriter.h simul.h sam_rsem_aux.h sampling.h boost/random.hpp WriteResults.h EM.cpp
+EM.o : utils.h my_assert.h Read.h SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h SingleHit.h PairedEndHit.h Model.h SingleModel.h SingleQModel.h PairedEndModel.h PairedEndQModel.h Refs.h GroupInfo.h HitContainer.h ReadIndex.h ReadReader.h Orientation.h LenDist.h RSPD.h QualDist.h QProfile.h NoiseQProfile.h ModelParams.h RefSeq.h RefSeqPolicy.h PolyARules.h Profile.h NoiseProfile.h Transcript.h Transcripts.h HitWrapper.h BamWriter.h simul.h sam_rsem_aux.h sampling.h WriteResults.h EM.cpp
 	$(CC) $(COFLAGS) EM.cpp
 
 BamConverter.h : utils.h my_assert.h sam_rsem_aux.h sam_rsem_cvt.h bc_aux.h Transcript.h Transcripts.h
@@ -104,14 +100,14 @@
 rsem-simulate-reads : simulation.o
 	$(CC) -o rsem-simulate-reads simulation.o
 
-simulation.o : utils.h Read.h SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h Model.h SingleModel.h SingleQModel.h PairedEndModel.h PairedEndQModel.h Refs.h RefSeq.h GroupInfo.h Transcript.h Transcripts.h Orientation.h LenDist.h RSPD.h QualDist.h QProfile.h NoiseQProfile.h Profile.h NoiseProfile.h simul.h boost/random.hpp WriteResults.h simulation.cpp
+simulation.o : utils.h Read.h SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h Model.h SingleModel.h SingleQModel.h PairedEndModel.h PairedEndQModel.h Refs.h RefSeq.h GroupInfo.h Transcript.h Transcripts.h Orientation.h LenDist.h RSPD.h QualDist.h QProfile.h NoiseQProfile.h Profile.h NoiseProfile.h simul.h WriteResults.h simulation.cpp
 	$(CC) $(COFLAGS) simulation.cpp
 
 rsem-run-gibbs : Gibbs.o
 	$(CC) -o rsem-run-gibbs Gibbs.o -lpthread
 
 #some header files are omitted
-Gibbs.o : utils.h my_assert.h boost/random.hpp sampling.h Model.h SingleModel.h SingleQModel.h PairedEndModel.h PairedEndQModel.h RefSeq.h RefSeqPolicy.h PolyARules.h Refs.h GroupInfo.h WriteResults.h Gibbs.cpp 
+Gibbs.o : utils.h my_assert.h sampling.h Model.h SingleModel.h SingleQModel.h PairedEndModel.h PairedEndQModel.h RefSeq.h RefSeqPolicy.h PolyARules.h Refs.h GroupInfo.h WriteResults.h Gibbs.cpp 
 	$(CC) $(COFLAGS) Gibbs.cpp
 
 Buffer.h : my_assert.h
@@ -120,7 +116,7 @@
 	$(CC) -o rsem-calculate-credibility-intervals calcCI.o -lpthread
 
 #some header files are omitted
-calcCI.o : utils.h my_assert.h boost/random.hpp sampling.h Model.h SingleModel.h SingleQModel.h PairedEndModel.h PairedEndQModel.h RefSeq.h RefSeqPolicy.h PolyARules.h Refs.h GroupInfo.h WriteResults.h Buffer.h calcCI.cpp
+calcCI.o : utils.h my_assert.h sampling.h Model.h SingleModel.h SingleQModel.h PairedEndModel.h PairedEndQModel.h RefSeq.h RefSeqPolicy.h PolyARules.h Refs.h GroupInfo.h WriteResults.h Buffer.h calcCI.cpp
 	$(CC) $(COFLAGS) calcCI.cpp
 
 rsem-get-unique : getUnique.cpp
