diff --git a/clipper/Makefile b/clipper/Makefile index 8e40bf1..dad4a7f 100644 --- a/clipper/Makefile +++ b/clipper/Makefile @@ -5,7 +5,6 @@ CC=g++ PREFIX?=/usr BINDIR?=$(PREFIX)/bin CFLAGS?=-O3 -I. -CXXFLAGS=-std=c++0x $(CFLAGS) # for debugging: # CFLAGS?=-g -I. @@ -71,7 +70,7 @@ $(PKG).${VER}-${REL}.tar.gz: $(PKG).tar.gz sparsehash: sparsehash-2.0.3 cd sparsehash-2.0.3; ./configure; make - mkdir -p sparsehash + mkdir sparsehash cp -r sparsehash-2.0.3/src/sparsehash/* sparsehash/ # why the libbam.a doesn't work? not sure... *.o works @@ -95,11 +94,8 @@ else $(CC) $(CFLAGS) fastq-lib.cpp tidx/tidx-lib.cpp -o $@ $< -lgsl -lgslcblas endif -fastq-multx: fastq-multx.cpp fastq-lib.cpp sparsehash - $(CC) $(CXXFLAGS) fastq-multx.cpp fastq-lib.cpp -o $@ - fastq-stats: fastq-stats.cpp fastq-lib.cpp gcModel.cpp sparsehash - $(CC) $(CXXFLAGS) fastq-lib.cpp gcModel.cpp -o $@ $< + $(CC) $(CFLAGS) fastq-lib.cpp gcModel.cpp -o $@ $< bam-filter: bam-filter.cpp $(CC) $(CFLAGS) fastq-lib.cpp -o $@ $< -lbamtools