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Makefile 6.89 KiB
# ==========================
# BEDTools Makefile
# (c) 2009 Aaron Quinlan
# ==========================
SHELL := /bin/bash -e
VERSION_FILE=./src/utils/version/version_git.h
RELEASED_VERSION_FILE=./src/utils/version/version_release.txt
# define our object and binary directories
export OBJ_DIR = obj
export BIN_DIR = bin
export SRC_DIR = src
export UTIL_DIR = src/utils
export CXX = g++
#ifeq ($(DEBUG),1)
#export CXXFLAGS = -Wall -O0 -g -fno-inline -fkeep-inline-functions -D_FILE_OFFSET_BITS=64 -fPIC -DDEBUG -D_DEBUG
#else
export CXXFLAGS = -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC
#endif
export LIBS = -lz
export BT_ROOT = src/utils/BamTools/
SUBDIRS = $(SRC_DIR)/annotateBed \
$(SRC_DIR)/bamToBed \
$(SRC_DIR)/bamToFastq \
$(SRC_DIR)/bedToBam \
$(SRC_DIR)/bedpeToBam \
$(SRC_DIR)/bedToIgv \
$(SRC_DIR)/bed12ToBed6 \
$(SRC_DIR)/closestBed \
$(SRC_DIR)/clusterBed \
$(SRC_DIR)/complementBed \
$(SRC_DIR)/coverageBed \
$(SRC_DIR)/expand \
$(SRC_DIR)/fastaFromBed \
$(SRC_DIR)/flankBed \
$(SRC_DIR)/genomeCoverageBed \
$(SRC_DIR)/getOverlap \
$(SRC_DIR)/groupBy \
$(SRC_DIR)/intersectFile \
$(SRC_DIR)/jaccard \
$(SRC_DIR)/linksBed \
$(SRC_DIR)/maskFastaFromBed \
$(SRC_DIR)/mapFile \
$(SRC_DIR)/mergeFile \
$(SRC_DIR)/multiBamCov \
$(SRC_DIR)/multiIntersectBed \
$(SRC_DIR)/nekSandbox1 \
$(SRC_DIR)/nucBed \
$(SRC_DIR)/pairToBed \
$(SRC_DIR)/pairToPair \
$(SRC_DIR)/randomBed \
$(SRC_DIR)/regressTest \
$(SRC_DIR)/reldist \
$(SRC_DIR)/sampleFile \
$(SRC_DIR)/shuffleBed \
$(SRC_DIR)/slopBed \
$(SRC_DIR)/sortBed \
$(SRC_DIR)/subtractBed \
$(SRC_DIR)/tagBam \
$(SRC_DIR)/unionBedGraphs \
$(SRC_DIR)/windowBed \
$(SRC_DIR)/windowMaker
UTIL_SUBDIRS = $(SRC_DIR)/utils/bedFile \ $(SRC_DIR)/utils/BinTree \
$(SRC_DIR)/utils/version \
$(SRC_DIR)/utils/bedGraphFile \
$(SRC_DIR)/utils/chromsweep \
$(SRC_DIR)/utils/Contexts \
$(SRC_DIR)/utils/FileRecordTools \
$(SRC_DIR)/utils/general \
$(SRC_DIR)/utils/gzstream \
$(SRC_DIR)/utils/fileType \
$(SRC_DIR)/utils/bedFilePE \
$(SRC_DIR)/utils/KeyListOps \
$(SRC_DIR)/utils/NewChromsweep \
$(SRC_DIR)/utils/sequenceUtilities \
$(SRC_DIR)/utils/tabFile \
$(SRC_DIR)/utils/BamTools \
$(SRC_DIR)/utils/BamTools-Ancillary \
$(SRC_DIR)/utils/BlockedIntervals \
$(SRC_DIR)/utils/Fasta \
$(SRC_DIR)/utils/VectorOps \
$(SRC_DIR)/utils/GenomeFile \
$(SRC_DIR)/utils/RecordOutputMgr
BUILT_OBJECTS = $(OBJ_DIR)/*.o
all: print_banner $(OBJ_DIR) $(BIN_DIR) autoversion $(UTIL_SUBDIRS) $(SUBDIRS)
@echo "- Building main bedtools binary."
@$(CXX) $(CXXFLAGS) -c src/bedtools.cpp -o obj/bedtools.o -I$(UTIL_DIR)/version/
@$(CXX) $(CXXFLAGS) -o $(BIN_DIR)/bedtools $(BUILT_OBJECTS) -L$(UTIL_DIR)/BamTools/lib/ -lbamtools $(LIBS) $(LDFLAGS)
@echo "done."
@echo "- Creating executables for old CLI."
@python scripts/makeBashScripts.py
@chmod +x bin/*
@echo "done."
.PHONY: all
print_banner:
@echo "Building BEDTools:"
@echo "========================================================="
.PHONY: print_banner
# make the "obj/" and "bin/" directories, if they don't exist
$(OBJ_DIR) $(BIN_DIR):
@mkdir -p $@
# One special case: All (or almost all) programs requires the BamTools API files to be created first.
.PHONY: bamtools_api
bamtools_api:
@$(MAKE) --no-print-directory --directory=$(BT_ROOT) api
$(UTIL_SUBDIRS) $(SUBDIRS): bamtools_api
# even though these are real directories, treat them as phony targets, forcing to always go in them are re-make.
# a future improvement would be the check for the compiled object, and rebuild only if the source code is newer.
.PHONY: $(UTIL_SUBDIRS) $(SUBDIRS)
$(UTIL_SUBDIRS) $(SUBDIRS): $(OBJ_DIR) $(BIN_DIR)
@echo "- Building in $@"
@$(MAKE) --no-print-directory --directory=$@
clean:
@$(MAKE) --no-print-directory --directory=$(BT_ROOT) clean_api
@echo " * Cleaning up."
@rm -f $(OBJ_DIR)/* $(BIN_DIR)/*
.PHONY: clean
test: all @cd test; bash test.sh
.PHONY: test
## For BEDTools developers (not users):
## When you want to release (and tag) a new version, run:
## $ make setversion VERSION=v2.17.2
## This will:
## 1. Update the "/src/utils/version/version_release.txt" file
## 2. Commit the file
## 3. Git-Tag the commit with the latest version
##
.PHONY: setversion
setversion:
ifeq "$(VERSION)" ""
$(error please set VERSION variable to the new version (e.g "make setversion VERSION=v2.17.2"))
endif
@echo "# This file was auto-generated by running \"make setversion VERSION=$(VERSION)\"" > "$(RELEASED_VERSION_FILE)"
@echo "# on $$(date) ." >> "$(RELEASED_VERSION_FILE)"
@echo "# Please do not edit or commit this file manually." >> "$(RELEASED_VERSION_FILE)"
@echo "#" >> "$(RELEASED_VERSION_FILE)"
@echo "$(VERSION)" >> $(RELEASED_VERSION_FILE)
@git add $(RELEASED_VERSION_FILE)
@git commit -q -m "Setting Release-Version $(VERSION)"
@git tag "$(VERSION)"
@echo "Version updated to $(VERSION)."
@echo ""
@echo "Don't forget to push the commits AND the tags:"
@echo " git push --all --tags"
@echo ""
## Automatic version detection
##
## What's going on here?
## 1. If there's a ".git" repository - use the version from the repository.
## ignore any released-version file. git repository is authorative.
##
## 2, If there's no ".git" repository,
## get the "released" version number from the release-version file.
##
## 2.1. If the current directory looks like "arq5x-bedtools-XXXXXXX",
## assume "-XXXXXX" is the last revision number (and the user
## probably downloaded the ZIP from github).
## Append the revision number to the released version string.
##
## 3. Compare the detected version (from steps 1,2) to the current string
## in ./src/utils/version/version_git.h .
## If they differ, update the header file - will cause a recompilation
## of version.o .
##
.PHONY: autoversion
autoversion:
@( \
if [ -d ".git" ] && which git > /dev/null ; then \
DETECTED_VERSION=$$(git describe --always --tags --dirty) ; \
else \
DETECTED_VERSION=$$(grep -v "^#" "$(RELEASED_VERSION_FILE)") ; \
if basename $$(pwd) | grep -q "^[[:alnum:]]*-bedtools-[[:alnum:]]*$$" ; then \
DETECTED_VERSION=$${DETECTED_VERSION}-zip-$$(basename "$$(pwd)" | sed 's/^[[:alnum:]]*-bedtools-//') ; \
fi ; \
fi ; \
\
CURRENT_VERSION="" ; \
[ -e "$(VERSION_FILE)" ] && CURRENT_VERSION=$$(grep "define VERSION_GIT " "$(VERSION_FILE)" | cut -f3 -d" " | sed 's/"//g') ; \
\
echo "DETECTED_VERSION = $$DETECTED_VERSION" ; \
echo "CURRENT_VERSION = $$CURRENT_VERSION" ; \
if [ "$${DETECTED_VERSION}" != "$${CURRENT_VERSION}" ] ; then \ echo "Updating version file." ; \
echo "#ifndef VERSION_GIT_H" > $(VERSION_FILE) ; \
echo "#define VERSION_GIT_H" >> $(VERSION_FILE) ; \
echo "#define VERSION_GIT \"$${DETECTED_VERSION}\"" >> $(VERSION_FILE) ; \
echo "#endif /* VERSION_GIT_H */" >> $(VERSION_FILE) ; \
fi )