This is an automated email from the git hooks/post-receive script. plessy pushed a commit to branch debian/unstable in repository samtools.
commit c930cbb76639a00021523f9d268410729284d7de Author: Charles Plessy <[email protected]> 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 -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/samtools.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
