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comparison BEDTools-Version-2.14.3/Makefile @ 0:dfcd8b6c1bda

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author aaronquinlan
date Thu, 03 Nov 2011 10:25:04 -0400
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-1:000000000000 0:dfcd8b6c1bda
1 # ==========================
2 # BEDTools Makefile
3 # (c) 2009 Aaron Quinlan
4 # ==========================
5
6 # define our object and binary directories
7 export OBJ_DIR = obj
8 export BIN_DIR = bin
9 export SRC_DIR = src
10 export CXX = g++
11 export CXXFLAGS = -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC
12 export LIBS = -lz
13 export BT_ROOT = src/utils/BamTools/
14
15
16 SUBDIRS = $(SRC_DIR)/annotateBed \
17 $(SRC_DIR)/bamToBed \
18 $(SRC_DIR)/bedToBam \
19 $(SRC_DIR)/bedToIgv \
20 $(SRC_DIR)/bed12ToBed6 \
21 $(SRC_DIR)/closestBed \
22 $(SRC_DIR)/complementBed \
23 $(SRC_DIR)/coverageBed \
24 $(SRC_DIR)/fastaFromBed \
25 $(SRC_DIR)/flankBed \
26 $(SRC_DIR)/genomeCoverageBed \
27 $(SRC_DIR)/intersectBed \
28 $(SRC_DIR)/linksBed \
29 $(SRC_DIR)/maskFastaFromBed \
30 $(SRC_DIR)/mergeBed \
31 $(SRC_DIR)/multiBamCov \
32 $(SRC_DIR)/multiIntersectBed \
33 $(SRC_DIR)/nucBed \
34 $(SRC_DIR)/overlap \
35 $(SRC_DIR)/pairToBed \
36 $(SRC_DIR)/pairToPair \
37 $(SRC_DIR)/shuffleBed \
38 $(SRC_DIR)/slopBed \
39 $(SRC_DIR)/sortBed \
40 $(SRC_DIR)/subtractBed \
41 $(SRC_DIR)/tagBam \
42 $(SRC_DIR)/unionBedGraphs \
43 $(SRC_DIR)/windowBed
44
45 UTIL_SUBDIRS = $(SRC_DIR)/utils/lineFileUtilities \
46 $(SRC_DIR)/utils/bedFile \
47 $(SRC_DIR)/utils/bedGraphFile \
48 $(SRC_DIR)/utils/chromsweep \
49 $(SRC_DIR)/utils/gzstream \
50 $(SRC_DIR)/utils/fileType \
51 $(SRC_DIR)/utils/bedFilePE \
52 $(SRC_DIR)/utils/sequenceUtilities \
53 $(SRC_DIR)/utils/tabFile \
54 $(SRC_DIR)/utils/BamTools \
55 $(SRC_DIR)/utils/BamTools-Ancillary \
56 $(SRC_DIR)/utils/Fasta \
57 $(SRC_DIR)/utils/genomeFile
58
59 all:
60 [ -d $(OBJ_DIR) ] || mkdir -p $(OBJ_DIR)
61 [ -d $(BIN_DIR) ] || mkdir -p $(BIN_DIR)
62
63 @echo "Building BEDTools:"
64 @echo "========================================================="
65
66 @for dir in $(UTIL_SUBDIRS); do \
67 echo "- Building in $$dir"; \
68 $(MAKE) --no-print-directory -C $$dir; \
69 echo ""; \
70 done
71
72 @for dir in $(SUBDIRS); do \
73 echo "- Building in $$dir"; \
74 $(MAKE) --no-print-directory -C $$dir; \
75 echo ""; \
76 done
77
78
79 .PHONY: all
80
81 clean:
82 @echo "Cleaning up."
83 @rm -f $(OBJ_DIR)/* $(BIN_DIR)/*
84 @rm -Rf $(BT_ROOT)/lib
85 @rm -f $(BT_ROOT)/src/api/*.o
86 @rm -f $(BT_ROOT)/src/api/internal/*.o
87 @rm -Rf $(BT_ROOT)/include
88
89 .PHONY: clean