[med-svn] samtools 07/07: Rely on the new upstream Makefile.

Charles Plessy plessy at moszumanska.debian.org
Fri Nov 22 09:55:50 UTC 2013 

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plessy pushed a commit to branch debian/unstable
in repository samtools.

commit c930cbb76639a00021523f9d268410729284d7de
Author: Charles Plessy <plessy at debian.org>
Date:   Fri Nov 22 18:54:01 2013 +0900

    Rely on the new upstream Makefile.
    
    For the moment it still needs to be extensively patched.
    
    diff --git a/Makefile b/Makefile
    index bf5557f..ec464d3 100644
    --- a/Makefile
    +++ b/Makefile
    @@ -50,7 +50,6 @@ all: $(PROGRAMS) $(BUILT_MISC_PROGRAMS)
    
     # Adjust $(HTSDIR) to point to your top-level htslib directory
     HTSDIR = ../htslib
    -include $(HTSDIR)/htslib.mk
     HTSLIB = $(HTSDIR)/libhts.a
    
    @@ -95,48 +94,48 @@ bgzip: bgzip.o $(HTSLIB)
    
     bam_h = bam.h $(htslib_bgzf_h) $(htslib_sam_h)
     bam2bcf_h = bam2bcf.h errmod.h
    -bam_tview_h = bam_tview.h $(bam_h) $(htslib_faidx_h) $(bam2bcf_h) sam_header.h $(HTSDIR)/htslib/khash.h
    +bam_tview_h = bam_tview.h $(bam_h) $(htslib_faidx_h) $(bam2bcf_h) sam_header.h $(HTSDIR)/khash.h
     sam_h = sam.h $(htslib_sam_h) $(bam_h)
    -sample_h = sample.h $(HTSDIR)/htslib/kstring.h
    +sample_h = sample.h $(HTSDIR)/kstring.h
    
     bam.o: bam.c $(bam_h) sam_header.h
    -bam2bcf.o: bam2bcf.c bam2bcf.h $(HTSDIR)/htslib/kfunc.h
    +bam2bcf.o: bam2bcf.c bam2bcf.h $(HTSDIR)/kfunc.h
     bam2bcf_indel.o: bam2bcf_indel.c bam2bcf.h
     bam2depth.o: bam2depth.c
     bam_aux.o: bam_aux.c
     bam_cat.o: bam_cat.c $(htslib_bgzf_h) $(bam_h)
     bam_color.o: bam_color.c $(bam_h)
    -bam_import.o: bam_import.c $(HTSDIR)/htslib/kstring.h $(bam_h) $(HTSDIR)/htslib/kseq.h
    +bam_import.o: bam_import.c $(HTSDIR)/kstring.h $(bam_h) $(HTSDIR)/kseq.h
     bam_index.o: bam_index.c $(bam_h)
    -bam_lpileup.o: bam_lpileup.c $(bam_h) $(HTSDIR)/htslib/ksort.h
    +bam_lpileup.o: bam_lpileup.c $(bam_h) $(HTSDIR)/ksort.h
     bam_mate.o: bam_mate.c $(bam_h)
     bam_md.o: bam_md.c $(htslib_faidx_h) $(sam_h) kaln.h kprobaln.h
     bam_pileup.o: bam_pileup.c $(sam_h)
     bam_plcmd.o: bam_plcmd.c $(sam_h) $(htslib_faidx_h) sam_header.h $(bam2bcf_h) $(sample_h)
     bam_reheader.o: bam_reheader.c $(htslib_bgzf_h) $(bam_h)
    -bam_rmdup.o: bam_rmdup.c $(sam_h) $(HTSDIR)/htslib/khash.h
    -bam_rmdupse.o: bam_rmdupse.c $(sam_h) $(HTSDIR)/htslib/khash.h $(HTSDIR)/htslib/klist.h
    -bam_sort.o: bam_sort.c $(bam_h) $(HTSDIR)/htslib/ksort.h
    +bam_rmdup.o: bam_rmdup.c $(sam_h) $(HTSDIR)/khash.h
    +bam_rmdupse.o: bam_rmdupse.c $(sam_h) $(HTSDIR)/khash.h $(HTSDIR)/klist.h
    +bam_sort.o: bam_sort.c $(bam_h) $(HTSDIR)/ksort.h
     bam_stat.o: bam_stat.c $(bam_h)
     bam_tview.o: bam_tview.c $(bam_tview_h)
     bam_tview_curses.o: bam_tview_curses.c $(bam_tview_h)
     bam_tview_html.o: bam_tview_html.c $(bam_tview_h)
    -bamshuf.o: bamshuf.c $(htslib_sam_h) $(HTSDIR)/htslib/ksort.h
    +bamshuf.o: bamshuf.c $(htslib_sam_h) $(HTSDIR)/ksort.h
     bamtk.o: bamtk.c $(bam_h) version.h samtools.h
    -bedcov.o: bedcov.c $(htslib_bgzf_h) $(bam_h) $(HTSDIR)/htslib/kseq.h
    -bedidx.o: bedidx.c $(HTSDIR)/htslib/ksort.h $(HTSDIR)/htslib/kseq.h $(HTSDIR)/htslib/khash.h
    +bedcov.o: bedcov.c $(htslib_bgzf_h) $(bam_h) $(HTSDIR)/kseq.h
    +bedidx.o: bedidx.c $(HTSDIR)/ksort.h $(HTSDIR)/kseq.h $(HTSDIR)/khash.h
     bgzip.o: bgzip.c $(htslib_bgzf_h)
     cut_target.o: cut_target.c $(bam_h) errmod.h $(htslib_faidx_h)
    -errmod.o: errmod.c errmod.h $(HTSDIR)/htslib/ksort.h
    +errmod.o: errmod.c errmod.h $(HTSDIR)/ksort.h
     kaln.o: kaln.c kaln.h
     kprobaln.o: kprobaln.c kprobaln.h
     padding.o: padding.c sam_header.h $(sam_h) $(bam_h) $(htslib_faidx_h)
    -phase.o: phase.c $(bam_h) errmod.h $(HTSDIR)/htslib/kseq.h $(HTSDIR)/htslib/khash.h $(HTSDIR)/htslib/ksort.h
    +phase.o: phase.c $(bam_h) errmod.h $(HTSDIR)/kseq.h $(HTSDIR)/khash.h $(HTSDIR)/ksort.h
     sam.o: sam.c $(htslib_faidx_h) $(sam_h)
    -sam_header.o: sam_header.c sam_header.h $(HTSDIR)/htslib/khash.h
    -sam_view.o: sam_view.c sam_header.h $(sam_h) $(htslib_faidx_h) $(HTSDIR)/htslib/khash.h
    -sample.o: sample.c $(sample_h) $(HTSDIR)/htslib/khash.h
    -stats.o: stats.c $(sam_h) sam_header.h khash_utils.h samtools.h $(HTSDIR)/htslib/khash.h $(htslib_faidx_h)
    +sam_header.o: sam_header.c sam_header.h $(HTSDIR)/khash.h
    +sam_view.o: sam_view.c sam_header.h $(sam_h) $(htslib_faidx_h) $(HTSDIR)/khash.h
    +sample.o: sample.c $(sample_h) $(HTSDIR)/khash.h
    +stats.o: stats.c $(sam_h) sam_header.h khash_utils.h samtools.h $(HTSDIR)/khash.h $(htslib_faidx_h)
    
     # test programs
    @@ -165,10 +164,10 @@ misc/md5sum-lite: misc/md5sum-lite.o
     misc/wgsim: misc/wgsim.o
            $(CC) $(LDFLAGS) -o $@ misc/wgsim.o $(LDLIBS) -lm -lz
    
    -misc/ace2sam.o: misc/ace2sam.c $(HTSDIR)/htslib/kstring.h $(HTSDIR)/htslib/kseq.h
    +misc/ace2sam.o: misc/ace2sam.c $(HTSDIR)/kstring.h $(HTSDIR)/kseq.h
     misc/md5.o: misc/md5.c misc/md5.h
    -misc/md5fa.o: misc/md5fa.c misc/md5.h $(HTSDIR)/htslib/kseq.h
    -misc/wgsim.o: misc/wgsim.c $(HTSDIR)/htslib/kseq.h
    +misc/md5fa.o: misc/md5fa.c misc/md5.h $(HTSDIR)/kseq.h
    +misc/wgsim.o: misc/wgsim.c $(HTSDIR)/kseq.h
    
     misc/maq2sam-short.o: misc/maq2sam.c
            $(CC) $(CFLAGS) $(CPPFLAGS) -c -o $@ misc/maq2sam.c
    @@ -189,7 +188,7 @@ install: $(PROGRAMS) $(BUILT_MISC_PROGRAMS)
     mostlyclean:
            -rm -f *.o misc/*.o version.h
    
    -clean: mostlyclean clean-htslib
    +clean: mostlyclean
            -rm -f $(PROGRAMS) libbam.a $(BUILT_MISC_PROGRAMS)
    
     distclean: clean
    (END)
---
 debian/rules             |   37 +++++++++++++++++++------------------
 debian/samtools.examples |    6 ------
 debian/samtools.install  |   17 +----------------
 3 files changed, 20 insertions(+), 40 deletions(-)

diff --git a/debian/rules b/debian/rules
index f4dc09e..0d119c6 100755
--- a/debian/rules
+++ b/debian/rules
@@ -1,24 +1,25 @@
 #!/usr/bin/make -f
 
-include /usr/share/cdbs/1/rules/debhelper.mk
-include /usr/share/cdbs/1/class/makefile.mk
-include /usr/share/cdbs/1/rules/patchsys-quilt.mk
+export DH_VERBOSE=1
 
-CFLAGS += -fPIC $(LDFLAGS) $(CPPFLAGS)
+%:
+	dh $@
 
-DEB_MAKE_BUILD_TARGET = all all-recur razip lib
-DEB_MAKE_CHECK_TARGET = -C examples all
+override_dh_auto_build:
+	dh_auto_build -- \
+	  HTSDIR="/usr/include/htslib" \
+	  HTSLIB=$(shell dpkg -S libhts.a | awk '{print $$2}') \
+	  CFLAGS="$$(dpkg-buildflags --get CFLAGS)" \
+	  CPPFLAGS="-I. -DSAMTOOLS=1 $$(dpkg-buildflags --get CPPFLAGS)" \
+	  LDFLAGS="$$(dpkg-buildflags --get LDFLAGS)"
 
-DEB_COMPRESS_EXCLUDE = .bam
-DEB_DH_BUILDDEB_ARGS = -- -Z=xz
-DEB_INSTALL_CHANGELOGS_ALL = NEWS
-clean::
-	$(RM) examples/calDepth examples/ex1.bam examples/ex1.bam.bai examples/ex1.fa.fai examples/ex1.glf examples/ex1.glfview.gz examples/ex1.pileup.gz examples/ex1a.bam examples/ex1b.bam examples/ex1f-rmduppe.bam examples/ex1f-rmdupse.bam examples/ex1f.bam examples/ex1f.rg examples/ex1.bcf
+override_dh_auto_test:
+	dh_auto_test -- \
+	  HTSDIR="/usr/include/htslib" \
+	  HTSLIB=$(shell dpkg -S libhts.a | awk '{print $$2}')
 
-binary-install/samtools::
-	install -m 644 bcftools/README $(CURDIR)/debian/samtools/usr/share/doc/samtools/README.bcftools
-	ln -s samtools.1.gz $(CURDIR)/debian/samtools/usr/share/man/man1/bcftools.1.gz
-	dh_bash-completion
-
-binary-fixup/samtools::
-	sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' $(CURDIR)/debian/samtools/usr/share/samtools/varfilter.py
+override_dh_auto_install:
+	dh_auto_install -- \
+	  prefix=/usr \
+	  HTSDIR="/usr/include/htslib" \
+	  HTSLIB=$(shell dpkg -S libhts.a | awk '{print $$2}')
diff --git a/debian/samtools.examples b/debian/samtools.examples
deleted file mode 100644
index 5a25472..0000000
--- a/debian/samtools.examples
+++ /dev/null
@@ -1,6 +0,0 @@
-examples/ex1.bam
-examples/ex1.fa
-examples/ex1.sam.gz
-examples/00README.txt
-examples/toy.fa
-examples/toy.sam
diff --git a/debian/samtools.install b/debian/samtools.install
index 7bd879b..7018f18 100644
--- a/debian/samtools.install
+++ b/debian/samtools.install
@@ -1,16 +1 @@
-#bgzip	usr/bin
-bcftools/bcftools	usr/bin
-razip	usr/bin
-samtools	usr/bin
-bcftools/vcfutils.pl	usr/share/samtools
-misc/*.pl	usr/share/samtools
-misc/*.py	usr/share/samtools
-misc/*.lua	usr/share/samtools
-misc/plot-bamcheck	usr/share/samtools
-misc/wgsim	usr/lib/samtools
-misc/ace2sam	usr/lib/samtools
-misc/bamcheck	usr/lib/samtools
-misc/maq2sam-long	usr/lib/samtools
-misc/maq2sam-short	usr/lib/samtools
-misc/md5fa		usr/lib/samtools
-misc/md5sum-lite	usr/lib/samtools
+test	usr/share/samtools

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