[med-svn] [rsem] 05/05: Use debian packaged samtools

[Andreas Tille]

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 <tille at debian.org>
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