This is an automated email from the git hooks/post-receive script. tille pushed a commit to branch master in repository rsem.
commit d27e227d4e1180eed88c0bb6af8c20a7b32344c5 Author: Andreas Tille <[email protected]> Date: Fri Dec 9 15:50:11 2016 +0100 Use debian packaged samtools --- debian/control | 3 +- debian/dirs | 1 + debian/patches/series | 1 + debian/patches/use_debian_packaged_samtools.patch | 70 +++++++++++++++++++++++ debian/rules | 4 +- 5 files changed, 76 insertions(+), 3 deletions(-) diff --git a/debian/control b/debian/control index 2a9c947..7deaf43 100644 --- a/debian/control +++ b/debian/control @@ -11,9 +11,10 @@ Build-Depends: debhelper (>= 9), perl, python, help2man, - bowtie | bowtie2 + libhts-dev, # bowtie is a run-time dependency available on only a few systems, not actually # needed for building but it prevents the creation of uninstallable packages + bowtie | bowtie2 Standards-Version: 3.9.8 Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/rsem.git Vcs-Git: https://anonscm.debian.org/git/debian-med/rsem.git diff --git a/debian/dirs b/debian/dirs new file mode 100644 index 0000000..e772481 --- /dev/null +++ b/debian/dirs @@ -0,0 +1 @@ +usr/bin diff --git a/debian/patches/series b/debian/patches/series index 997a9fc..48dac3a 100644 --- a/debian/patches/series +++ b/debian/patches/series @@ -1 +1,2 @@ hardening +use_debian_packaged_samtools.patch diff --git a/debian/patches/use_debian_packaged_samtools.patch b/debian/patches/use_debian_packaged_samtools.patch new file mode 100644 index 0000000..18cc0c9 --- /dev/null +++ b/debian/patches/use_debian_packaged_samtools.patch @@ -0,0 +1,70 @@ +--- a/Makefile ++++ b/Makefile +@@ -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-ca + + .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 diff --git a/debian/rules b/debian/rules index 0523d73..302f3c5 100755 --- a/debian/rules +++ b/debian/rules @@ -27,9 +27,9 @@ override_dh_auto_build: debian/rsem-simulate-reads.1 override_dh_auto_install: - find . -maxdepth 1 -type f -perm /u+x | xargs -n 1 -I{} dh_install {} /usr/bin/ + #find . -maxdepth 1 -type f -perm /u+x | xargs -n 1 -I{} dh_install {} /usr/bin/ dh_install rsem_perl_utils.pm /usr/share/perl5 - dh_auto_install -- BOOST=/usr/include prefix=debian/tmp + dh_auto_install -- BOOST=/usr/include prefix="/usr" get-orig-source: uscan --verbose --force-download --repack --compression xz -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/rsem.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
