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| author | Andreas Tille <tille@debian.org> | 2021-09-09 08:01:13 +0200 |
|---|---|---|
| committer | Andreas Tille <tille@debian.org> | 2021-09-09 08:01:13 +0200 |
| commit | bfae2823a9ac6672748c3e9d405fa0558896f44a (patch) | |
| tree | 5834c881a66233c690ac0f366341b42e337170ae | |
| parent | 28c8dfb9efed208e5ee58fb9525e9f10d008f265 (diff) | |
Use Debian packaged samtools
Last-Update: Fri, 09 Dec 2016 14:26:08 +0100
Gbp-Pq: Name use_debian_packaged_samtools.patch
| -rw-r--r-- | Makefile | 22 |
1 files changed, 9 insertions, 13 deletions
@@ -12,7 +12,7 @@ BOOST = . # Compilation variables CXX = g++ -CXXFLAGS += -std=gnu++98 -Wall -I. -I$(BOOST) -I$(SAMTOOLS)/$(HTSLIB) +CXXFLAGS += -std=gnu++98 -Wall -I. -I$(BOOST) CPPFLAGS ?= LDFLAGS ?= @@ -30,8 +30,8 @@ exec_prefix = $(prefix) bindir = $(exec_prefix)/bin # Auxiliary variables for compilation -SAMHEADERS = $(SAMTOOLS)/$(HTSLIB)/htslib/sam.h -SAMLIBS = $(SAMTOOLS)/$(HTSLIB)/libhts.a +SAMHEADERS = +SAMLIBS = CONFIGURE = ./configure OBJS1 = parseIt.o @@ -54,12 +54,12 @@ SCRIPTS = rsem-prepare-reference rsem-calculate-expression rsem-refseq-extract-p .PHONY : all ebseq pRSEM clean -all : $(PROGRAMS) $(SAMTOOLS)/samtools +all : $(PROGRAMS) $(SAMTOOLS)/samtools : cd $(SAMTOOLS) && $(CONFIGURE) --without-curses && $(MAKE) -f $(SAMTOOLS_MAKEFILE) samtools -$(SAMLIBS) : $(SAMTOOLS)/samtools +$(SAMLIBS) : # Compile objects @@ -78,10 +78,10 @@ $(PROGS1) : $(CXX) $(LDFLAGS) -o $@ $^ $(LDLIBS) $(PROGS2) : - $(CXX) $(LDFLAGS) -pthread -o $@ $^ $(LDLIBS) -lz + $(CXX) $(LDFLAGS) -pthread -o $@ $^ $(LDLIBS) -lhts -lz $(PROGS3) : - $(CXX) $(LDFLAGS) -pthread -o $@ $^ $(LDLIBS) + $(CXX) $(LDFLAGS) -pthread -o $@ $^ $(LDLIBS) -lhts # Dependencies for executables @@ -163,17 +163,13 @@ pRSEM : # Install RSEM -install : $(PROGRAMS) $(SCRIPTS) $(SAMTOOLS)/samtools rsem_perl_utils.pm - $(INSTALL_DIR) $(DESTDIR)$(bindir) $(DESTDIR)$(bindir)/$(SAMTOOLS) - $(foreach prog,$(PROGRAMS),$(INSTALL_PROGRAM) $(prog) $(DESTDIR)$(bindir)/$(prog) ; $(STRIP) $(DESTDIR)$(bindir)/$(prog) ;) - $(INSTALL_PROGRAM) $(SAMTOOLS)/samtools $(DESTDIR)$(bindir)/$(SAMTOOLS)/samtools - $(STRIP) $(DESTDIR)$(bindir)/$(SAMTOOLS)/samtools +install : $(PROGRAMS) $(SCRIPTS) rsem_perl_utils.pm + $(foreach prog,$(PROGRAMS),$(INSTALL_PROGRAM) $(prog) $(DESTDIR)$(bindir)/$(prog) ; ) $(foreach script,$(SCRIPTS),$(INSTALL_PROGRAM) $(script) $(DESTDIR)$(bindir)/$(script) ;) $(INSTALL_DATA) rsem_perl_utils.pm $(DESTDIR)$(bindir)/rsem_perl_utils.pm # Clean clean : rm -f *.o *~ $(PROGRAMS) - cd $(SAMTOOLS) && $(MAKE) clean-all cd EBSeq && $(MAKE) clean cd pRSEM && $(MAKE) clean |