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 <ti...@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 You're receiving this email because of your account on salsa.debian.org.
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