Permalink
Cannot retrieve contributors at this time
Fetching contributors…
Cannot retrieve contributors at this time
| # | |
| # $Id$ | |
| CC=g++ | |
| PREFIX?=/usr | |
| BINDIR?=$(PREFIX)/bin | |
| CFLAGS?=-O3 -I. | |
| # for debugging: | |
| # CFLAGS?=-g -I. | |
| PKG=ea-utils | |
| REL := $(shell svnversion 2>/dev/null | perl -ne 'print $$1 if /(\d+)/' ) | |
| VER := $(shell grep '%define ver' ${PKG}.spec | perl -ne 'print $$1 if / (\S+) *$$/') | |
| SRC=fastq-clipper.cpp fastq-mcf.cpp fastq-multx.cpp fastq-join.cpp fastq-stats.cpp gcModel.cpp | |
| BIN=fastq-mcf fastq-multx fastq-join fastq-stats fastq-clipper sam-stats varcall | |
| TOOLS=fastx-graph gtf2bed determine-phred randomFQ alc | |
| all: $(BIN) check | |
| debug: | |
| CFLAGS="-g -I." ${MAKE} $(MFLAGS) varcall | |
| install: $(BIN) $(BINDIR)/fastq-clipper $(BINDIR)/fastq-mcf $(BINDIR)/fastq-multx $(BINDIR)/fastq-join $(BINDIR)/fastq-stats $(BINDIR)/sam-stats $(BINDIR)/varcall $(BINDIR)/fastx-graph $(BINDIR)/determine-phred $(BINDIR)/randomFQ $(BINDIR)/alc | |
| $(BINDIR): | |
| mkdir -p $(BINDIR) | |
| $(BINDIR)/%: % $(BINDIR) | |
| cp $< $@ | |
| dist: getrel $(PKG).${VER}-${REL}.tar.gz | |
| # these shenanigans are done to ensure than the release in the spec file is the same as the subversion release | |
| # a less verbose way should be possible | |
| getrel: | |
| grep "${REL}" $(PKG).spec || touch $(PKG).spex | |
| .PHONY: getrel debug $(PKG).spec | |
| $(PKG).spec: | |
| perl -pe 's/%RELEASE%/${REL}/' $(PKG).spex > $(PKG).spec | |
| $(PKG).tar.gz: Makefile $(TOOLS) $(SRC) $(PKG).spec fastq-lib.cpp fastq-lib.h sam-stats.cpp fastq-stats.cpp gcModel.cpp gcModel.h varcall.cpp utils.h README CHANGES sparsehash-2.0.3 samtools/*.c t | |
| rm -rf $(PKG).${VER}-${REL} | |
| mkdir $(PKG).${VER}-${REL} | |
| mkdir $(PKG).${VER}-${REL}/tidx | |
| mkdir $(PKG).${VER}-${REL}/samtools | |
| cp -nr $^ $(PKG).${VER}-${REL} | |
| cp -nr tidx/*.cpp tidx/*.h $(PKG).${VER}-${REL}/tidx | |
| cp -nr samtools/*.c samtools/*.h samtools/Makefile $(PKG).${VER}-${REL}/samtools | |
| tar --exclude=".svn" -cvzf $(PKG).tar.gz $(PKG).${VER}-${REL} | |
| rm -rf $(PKG).${VER}-${REL} | |
| check: $(BIN) | |
| prove -j 4 t | |
| disttest: $(PKG).tar.gz | |
| rm -rf $(PKG).${VER}-${REL} | |
| tar -xzvf $(PKG).tar.gz | |
| cd $(PKG).${VER}-${REL} && make check | |
| rm -rf $(PKG).${VER}-${REL} | |
| $(PKG).${VER}-${REL}.tar.gz: $(PKG).tar.gz | |
| cp $< $@ | |
| %: %.cpp fastq-lib.cpp fastq-lib.h sparsehash | |
| $(CC) $(CFLAGS) $< fastq-lib.cpp -o $@ | |
| sparsehash: sparsehash-2.0.3 | |
| cd sparsehash-2.0.3; ./configure; make | |
| mkdir sparsehash | |
| cp -r sparsehash-2.0.3/src/sparsehash/* sparsehash/ | |
| # why the libbam.a doesn't work? not sure... *.o works | |
| sam-stats: sam-stats.cpp samtools/libbam.a samtools/bam.h fastq-lib.h sparsehash | |
| ifeq ($(OS),Windows_NT) | |
| $(CC) $(CFLAGS) samtools/*.o -lz -lpthread -lws2_32 fastq-lib.cpp $< -o $@ | |
| else | |
| $(CC) $(CFLAGS) samtools/*.o -lz -lpthread fastq-lib.cpp $< -o $@ | |
| endif | |
| samtools/libbam.a: samtools/*.c samtools/*.h | |
| cd samtools && make libbam.a | |
| ea-bcl2fastq: ea-bcl2fastq.cpp | |
| $(CC) $(CFLAGS) $< -lz -o $@ | |
| varcall: varcall.cpp fastq-lib.cpp tidx/tidx-lib.cpp sparsehash | |
| ifeq ($(OS),Windows_NT) | |
| echo varcall: not supported yet | |
| else | |
| $(CC) $(CFLAGS) fastq-lib.cpp tidx/tidx-lib.cpp -o $@ $< -lgsl -lgslcblas | |
| endif | |
| fastq-stats: fastq-stats.cpp fastq-lib.cpp gcModel.cpp sparsehash | |
| $(CC) $(CFLAGS) fastq-lib.cpp gcModel.cpp -o $@ $< | |
| bam-filter: bam-filter.cpp | |
| $(CC) $(CFLAGS) fastq-lib.cpp -o $@ $< -lbamtools | |
| clean: | |
| rm -f *.o $(BIN) | |
| cd samtools && make clean |