diff options
| author | Calvin Morrison <mutantturkey@gmail.com> | 2013-10-18 10:26:12 -0400 |
|---|---|---|
| committer | Calvin Morrison <mutantturkey@gmail.com> | 2013-10-18 10:26:12 -0400 |
| commit | c1a34163771229aa269ada443c6baa38f3073c11 (patch) | |
| tree | daa87dd67e45ad910f750587e4769acda68e9eec /src/c/Makefile | |
| parent | 2f62ad7c4ec7ed5bae74c4444442dd871222e6c6 (diff) | |
add kmercounting code from dna-utils. update our make file to support debugging, and update quikr to count-kmer code internally
Diffstat (limited to 'src/c/Makefile')
| -rw-r--r-- | src/c/Makefile | 32 |
1 files changed, 21 insertions, 11 deletions
diff --git a/src/c/Makefile b/src/c/Makefile index e927b13..1f59312 100644 --- a/src/c/Makefile +++ b/src/c/Makefile @@ -1,17 +1,27 @@ VERSION=\"v1.0.4\" UNAME := $(shell uname) CC = gcc -QUIKR_TRAIN_CFLAGS = -O3 -s -mtune=native -Wall -lm -lz -D$(UNAME) -DVERSION=$(VERSION) -MULTIFASTA_CFLAGS = -O3 -s -mtune=native -Wextra -Wall -lm -lz -pthread -L../ -I../ -std=gnu99 -fopenmp -D$(UNAME) -DVERSION=$(VERSION) -QUIKR_CFLAGS= -O3 -s -mtune=native -Wextra -Wall -lm -lz -std=gnu99 -D$(UNAME) -DVERSION=$(VERSION) +QUIKR_TRAIN_CFLAGS = -D$(UNAME) -DVERSION=$(VERSION) +MULTIFASTA_CFLAGS = -pthread -L../ -I../ -std=gnu99 -fopenmp -D$(UNAME) -DVERSION=$(VERSION) +QUIKR_CFLAGS = -std=gnu99 -D$(UNAME) -DVERSION=$(VERSION) -all: quikr_train_ quikr_ multifasta_to_otu_ +ifndef DEBUG +CFLAGS = -O3 -s -mtune=native -Wextra -Wall -lm -lz +else +CFLAGS = -ggdb3 -O0 -Wall -Wextra -lm -lz +endif -multifasta_to_otu_: - $(CC) multifasta_to_otu.c quikr_functions.c nnls.c -o multifasta_to_otu $(MULTIFASTA_CFLAGS) -quikr_train_: - $(CC) quikr_train.c quikr_functions.c -o quikr_train $(QUIKR_TRAIN_CFLAGS) -quikr_: - $(CC) quikr.c quikr_functions.c nnls.c -o quikr $(QUIKR_CFLAGS) -I../ +all: nnls.o kmer_utils.o quikr_train quikr multifasta_to_otu + +nnls.o: nnls.c + $(CC) -c nnls.c -o nnls.o $(CFLAGS) +kmer_utils.o: kmer_utils.c + $(CC) -c kmer_utils.c -o kmer_utils.o $(CFLAGS) +multifasta_to_otu: kmer_utils.o nnls.o multifasta_to_otu.c + $(CC) multifasta_to_otu.c quikr_functions.c nnls.o kmer_utils.o -o multifasta_to_otu $(CFLAGS) $(MULTIFASTA_CFLAGS) +quikr_train: kmer_utils.o quikr_train.c + $(CC) quikr_train.c quikr_functions.c -o quikr_train $(CFLAGS) $(QUIKR_TRAIN_CFLAGS) +quikr: kmer_utils.o nnls.o quikr.c + $(CC) quikr.c quikr_functions.c nnls.o kmer_utils.o -o quikr $(CFLAGS) $(QUIKR_CFLAGS) -I../ clean: - rm -vf quikr_train quikr multifasta_to_otu + rm -vf quikr_train quikr multifasta_to_otu *.o |