forked from zeeev/wham
-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathMakefile
49 lines (38 loc) · 2 KB
/
Makefile
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
######################################
# Makefile written by Zev Kronenberg #
# zev.kronenberg@gmail.com #
######################################
CC=g++
GCC=gcc
GIT_VERSION := $(shell git describe --abbrev=4 --dirty --always)
CFLAGS= -g -Wall -DVERSION=\"$(GIT_VERSION)\" -std=c++0x #-D_NO_RAZF
INCLUDE=-Isrc/lib -Isrc/bamtools/include -Isrc/bamtools/src -Isrc/ -Isrc/fastahack -Isrc/Complete-Striped-Smith-Waterman-Library/src/ -Isrc/seqan/core/include/ -Isrc/seqan/extras/include
OUTFOLD=bin/
LIBS=-L./ -lbamtools -fopenmp -lz -lm
RUNTIME=-Wl,-rpath=src/bamtools/lib/
all: mvSSW createBin bamtools libbamtools.a buildWHAMBAM clean
debug: mvSSW createBin bamtools libbamtools.a buildWHAMBAMD clean
mvSSW:
cp src/lib/ssw.c src/Complete-Striped-Smith-Waterman-Library/src
createBin:
-mkdir bin
bamtools:
cd src/bamtools && mkdir -p build && cd build && cmake .. && make
libbamtools.a: bamtools
cp src/bamtools/lib/libbamtools.a .
FASTA.o:
cd src/fastahack && make
ssw_cpp.o:
cd src/Complete-Striped-Smith-Waterman-Library/src && make
SSW = src/Complete-Striped-Smith-Waterman-Library/src/ssw_cpp.o src/Complete-Striped-Smith-Waterman-Library/src/ssw.o
FASTAHACK = src/fastahack/Fasta.o
buildWHAMBAM: libbamtools.a FASTA.o ssw_cpp.o
$(CC) $(CFLAGS) src/lib/*cpp src/bin/multi-wham-testing.cpp $(INCLUDE) $(LIBS) $(FASTAHACK) $(SSW) -o $(OUTFOLD)WHAM-BAM $(RUNTIME)
buildWHAMBAMD: libbamtools.a FASTA.o ssw_cpp.o
$(CC) $(CFLAGS) -g -DDEBUG src/lib/*cpp src/bin/multi-wham-testing.cpp $(INCLUDE) $(LIBS) $(FASTAHACK) $(SSW) -o $(OUTFOLD)WHAM-BAM $(RUNTIME)
buildWHAMDUMPER:
$(CC) $(CFLAGS) -g src/lib/*cpp src/bin/multi-wham.cpp $(INCLUDE) $(LIBS) -o $(OUTFOLD)WHAM-BAM-DUMPER $(RUNTIME)
buildWHAMBAMGENE:
$(CC) $(CFLAGS) -g src/lib/*cpp src/bin/multi-wham-testing-gene.cpp $(INCLUDE) $(LIBS) -o $(OUTFOLD)WHAM-BAM-GENE $(RUNTIME)
clean:
-@rm *.a