[med-svn] [Git][med-team/lumpy-sv][master] Try hard to use Debian packaged libs - but I have no idea how to prevent bedtools code copy

[Andreas Tille]

Andreas Tille pushed to branch master at Debian Med / lumpy-sv


Commits:
8df1c62c by Andreas Tille at 2020-05-26T18:03:26+02:00
Try hard to use Debian packaged libs - but I have no idea how to prevent bedtools code copy

- - - - -


3 changed files:

- debian/changelog
- + debian/patches/series
- + debian/patches/use_debian_packaged_libs.patch


Changes:

=====================================
debian/changelog
=====================================
@@ -2,5 +2,13 @@ lumpy-sv (0.3.0+dfsg-1) UNRELEASED; urgency=medium
 
   * Initial release (Closes: #<bug>)
   TODO: https://github.com/hall-lab/bamkit
+  
+  TODO2: argh, bedtools code copy is linked here - so the removal does not really work
+    src/lumpy/SV_Bedpe.cpp:#include "BamAncillary.h"
+    src/lumpy/SV_SplitRead.cpp:#include "BamAncillary.h"
+    src/lumpy/lumpy.cpp:#include "BamAncillary.h"
+    src/lumpy/bp_softclip_fa.cpp:#include "BamAncillary.h"
+    src/lumpy/SV_Pair.cpp:#include "BamAncillary.h"
+
 
  -- Andreas Tille <tille at debian.org>  Tue, 26 May 2020 15:07:58 +0200


=====================================
debian/patches/series
=====================================
@@ -0,0 +1 @@
+use_debian_packaged_libs.patch


=====================================
debian/patches/use_debian_packaged_libs.patch
=====================================
@@ -0,0 +1,111 @@
+--- a/Makefile
++++ b/Makefile
+@@ -50,13 +50,13 @@ lumpy:
+ 	@echo "Building lumpy:"
+ 	@echo "========================================================="
+ 
+-	@$(MAKE) --no-print-directory --directory=$(BT_ROOT) api
++	#@$(MAKE) --no-print-directory --directory=$(BT_ROOT) api
+ 
+-	@for dir in $(UTIL_SUBDIRS); do \
+-		echo "- Building in $$dir"; \
+-		$(MAKE) --no-print-directory -C $$dir; \
+-		echo ""; \
+-	done
++	#@for dir in $(UTIL_SUBDIRS); do \
++	#	echo "- Building in $$dir"; \
++	#	$(MAKE) --no-print-directory -C $$dir; \
++	#	echo ""; \
++	#done
+ 
+ 	@for dir in $(SUBDIRS); do \
+ 		echo "- Building in $$dir"; \
+@@ -64,7 +64,7 @@ lumpy:
+ 		echo ""; \
+ 	done
+ 
+-lumpy_filter: htslib
++lumpy_filter: # htslib - use Debian packaged htslib
+ 	[ -d $(BIN_DIR) ] || mkdir -p $(BIN_DIR)
+ 	$(MAKE) --no-print-directory -C src/filter/
+ 	cp src/filter/lumpy_filter $(BIN_DIR)
+@@ -100,9 +100,9 @@ lumpyexpress:
+ clean:
+ 	@echo "Cleaning up."
+ 	@rm -f $(OBJ_DIR)/* $(BIN_DIR)/*
+-	@rm -Rf $(BT_ROOT)/lib
+-	@rm -f $(BT_ROOT)/src/api/*.o
+-	@rm -f $(BT_ROOT)/src/api/internal/*.o
+-	@rm -Rf $(BT_ROOT)/include
++	#@rm -Rf $(BT_ROOT)/lib
++	#@rm -f $(BT_ROOT)/src/api/*.o
++	#@rm -f $(BT_ROOT)/src/api/internal/*.o
++	#@rm -Rf $(BT_ROOT)/include
+ 
+ .PHONY: clean
+--- a/src/lumpy/Makefile
++++ b/src/lumpy/Makefile
+@@ -5,18 +5,10 @@ BIN_DIR = ../../bin/
+ # -------------------
+ # define our includes
+ # -------------------
+-INCLUDES = -I$(UTILITIES_DIR)/bedFile/ \
+-           -I$(UTILITIES_DIR)/bedFilePE/ \
+-           -I$(UTILITIES_DIR)/genomeFile/ \
+-           -I$(UTILITIES_DIR)/version/ \
+-           -I$(UTILITIES_DIR)/gzstream/ \
+-           -I$(UTILITIES_DIR)/lineFileUtilities/ \
+-           -I$(UTILITIES_DIR)/fileType/ \
+-           -I$(UTILITIES_DIR)/BamTools/include \
+-		   -I$(UTILITIES_DIR)/BamTools-Ancillary \
+-           -I$(UTILITIES_DIR)/sequenceUtilities \
+-           -I$(UTILITIES_DIR)/UCSCBins \
+-           -I$(UTILITIES_DIR)/sqlite3 
++INCLUDES = -I/usr/include/bamtools \
++           -I/usr/include/fastahack \
++           -I$(UTILITIES_DIR)/version \
++           -I$(UTILITIES_DIR)/UCSCBins
+ 
+ # ----------------------------------
+ # define our source and object files
+@@ -55,7 +47,7 @@ all: $(PROGRAM)
+ $(PROGRAM): $(BUILT_OBJECTS) $(EXT_OBJECTS)
+ 	@echo "  * linking $(PROGRAM)"
+ 	@$(CXX) $(LDFLAGS) $(CXXFLAGS) -o $(BIN_DIR)/$@ $^ \
+-		-L$(UTILITIES_DIR)/BamTools/lib/ -lbamtools \
++		-lbamtools \
+ 		$(LIBS) \
+ 		-lz -lm -ldl -lpthread
+ 
+@@ -64,14 +56,15 @@ $(OBJ_DIR)/%.o: %.cpp
+ 	@$(CXX) -g  -c $(CXXFLAGS) $(LDFLAGS) $(INCLUDES) $< -o $@
+ 
+ $(EXT_OBJECTS):
+-	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/BamTools-Ancillary/
+-	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/BamTools/
+-	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/bedFilePE/
+-	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/sequenceUtilities/
+-	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/lineFileUtilities/
+-	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/gzstream/
+-	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/fileType/ 
+-	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/sqlite3/ 
++	#@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/BamTools-Ancillary/
++	#@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/BamTools/
++	#@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/bedFilePE/
++	#@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/sequenceUtilities/
++	#@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/lineFileUtilities/
++	#@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/gzstream/
++	#@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/fileType/ 
++	#@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/sqlite3/
++	echo "Use Debian packaged bamtools bedtools gzstream and sqlite3"
+ 
+ clean:
+ 	@echo "Cleaning up."
+--- a/src/filter/Makefile
++++ b/src/filter/Makefile
+@@ -1,4 +1,4 @@
+ 
+ all:
+-	$(CC) -I../../lib/htslib/ -o lumpy_filter filter.c ../../lib/htslib/libhts.a -lcrypto -lcurl -lpthread -lz
++	$(CC) -I/usr/include/htslib -o lumpy_filter filter.c -lhts -lcrypto -lcurl -lpthread -lz
+ 



View it on GitLab: https://salsa.debian.org/med-team/lumpy-sv/-/commit/8df1c62c3a5aae8612b1b5ae88724d03b73817d7

-- 
View it on GitLab: https://salsa.debian.org/med-team/lumpy-sv/-/commit/8df1c62c3a5aae8612b1b5ae88724d03b73817d7
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