[med-svn] [libvcflib] 06/07: Use debian packaged libsmithwatermann

[Andreas Tille]

This is an automated email from the git hooks/post-receive script.

tille pushed a commit to branch master
in repository libvcflib.

commit bdcf5e1171893c703578ce5c9b5a1008941a626e
Author: Andreas Tille <tille at debian.org>
Date:   Wed Jun 22 16:59:43 2016 +0200

    Use debian packaged libsmithwatermann
---
 debian/control                              |  3 +-
 debian/patches/ignore_smith_watermann.patch | 46 +++++++++++++++++++++++++++++
 debian/patches/series                       |  1 +
 3 files changed, 49 insertions(+), 1 deletion(-)

diff --git a/debian/control b/debian/control
index d1d2d23..1418366 100644
--- a/debian/control
+++ b/debian/control
@@ -5,7 +5,8 @@ Section: science
 Priority: optional
 Build-Depends: debhelper (>= 9),
                python-markdown,
-               libtabixpp-dev
+               libtabixpp-dev,
+               libsmithwaterman-dev
 Standards-Version: 3.9.8
 Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/libvcflib.git
 Vcs-Git: https://anonscm.debian.org/git/debian-med/libvcflib.git
diff --git a/debian/patches/ignore_smith_watermann.patch b/debian/patches/ignore_smith_watermann.patch
new file mode 100644
index 0000000..7479d0c
--- /dev/null
+++ b/debian/patches/ignore_smith_watermann.patch
@@ -0,0 +1,46 @@
+--- a/Makefile
++++ b/Makefile
+@@ -156,17 +156,20 @@ $(OBJECTS): $(SOURCES) $(HEADERS) $(TABI
+ 	$(CXX) -c -o $@ src/$(*F).cpp $(INCLUDES) $(LDFLAGS) $(CXXFLAGS) && cp src/*.h* $(VCF_LIB_LOCAL)/$(INC_DIR)/
+ 
+ multichoose: pre
+-	cd multichoose && $(MAKE) && cp *.h* $(VCF_LIB_LOCAL)/$(INC_DIR)/
++	echo "Source does not contain dir multichoose"
++	# cd multichoose && $(MAKE) && cp *.h* $(VCF_LIB_LOCAL)/$(INC_DIR)/
+ 
+ intervaltree: pre
+-	cd intervaltree && $(MAKE) && cp *.h* $(VCF_LIB_LOCAL)/$(INC_DIR)/
++	echo "Source does not contain dir intervaltree"
++	# cd intervaltree && $(MAKE) && cp *.h* $(VCF_LIB_LOCAL)/$(INC_DIR)/
+ 
+ $(TABIX): pre
+ 	echo "No need to create separately packaged tabixpp"
+ 	# cd tabixpp && $(MAKE) && cp *.h* $(VCF_LIB_LOCAL)/$(INC_DIR)/
+ 
+ $(SMITHWATERMAN): pre
+-	cd smithwaterman && $(MAKE) && cp *.h* $(VCF_LIB_LOCAL)/$(INC_DIR)/ && cp *.o $(VCF_LIB_LOCAL)/$(OBJ_DIR)/
++	echo "Source does not contain dir smithwaterman"
++	# cd smithwaterman && $(MAKE) && cp *.h* $(VCF_LIB_LOCAL)/$(INC_DIR)/ && cp *.o $(VCF_LIB_LOCAL)/$(OBJ_DIR)/
+ 
+ $(DISORDER): $(SMITHWATERMAN)
+ 
+@@ -183,7 +186,8 @@ $(FASTAHACK): pre
+ #	cd fsom && $(CXX) $(CXXFLAGS) -c fsom.c -lm
+ 
+ $(FILEVERCMP): pre
+-	cd filevercmp && make && cp *.h* $(VCF_LIB_LOCAL)/$(INC_DIR)/ && cp *.o $(VCF_LIB_LOCAL)/$(INC_DIR)/
++	echo "Source does not contain dir filevercmp"
++	# cd filevercmp && make && cp *.h* $(VCF_LIB_LOCAL)/$(INC_DIR)/ && cp *.o $(VCF_LIB_LOCAL)/$(INC_DIR)/
+ 
+ $(SHORTBINS): pre
+ 	$(MAKE) bin/$@
+@@ -220,7 +224,7 @@ clean:
+ 	rm -rf $(INC_DIR)
+ 	rm -rf $(OBJ_DIR)
+ 	# cd tabixpp && make clean
+-	cd smithwaterman && make clean
+-	cd fastahack && make clean
++	# cd smithwaterman && make clean
++	# cd fastahack && make clean
+ 
+ .PHONY: clean all test pre
diff --git a/debian/patches/series b/debian/patches/series
index 37e6a7c..06233fc 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1 +1,2 @@
 use_debian_packaged_tabixpp.patch
+ignore_smith_watermann.patch

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