1 files changed, 0 insertions, 62 deletions
diff --git a/biology/freebayes/files/patch-src_Makefile b/biology/freebayes/files/patch-src_Makefile
deleted file mode 100644
index cfe34b3b4ead..000000000000
--- a/biology/freebayes/files/patch-src_Makefile
+++ /dev/null
@@ -1,62 +0,0 @@
---- src/Makefile.orig	2018-03-23 14:01:01 UTC
-+++ src/Makefile
-@@ -5,8 +5,9 @@
- ################################################################################
- 
- # Compiler
--CXX=g++ ${CXXFLAGS}
--C=gcc
-+CXX ?= g++
-+# CXX += ${CXXFLAGS}
-+CC ?= gcc
- 
- export CXXFLAGS
- export C
-@@ -17,7 +18,7 @@ export LIBFLAGS
- 
- # Compiler flags
- 
--CFLAGS=-O3 -D_FILE_OFFSET_BITS=64 -g
-+CFLAGS += -D_FILE_OFFSET_BITS=64
- #CFLAGS=-O3 -static -D VERBOSE_DEBUG  # enables verbose debugging via --debug2
- 
- SEQLIB_ROOT=../SeqLib
-@@ -25,7 +26,7 @@ VCFLIB_ROOT=../vcflib
- TABIX_ROOT=$(VCFLIB_ROOT)/tabixpp
- HTSLIB_ROOT=$(SEQLIB_ROOT)/htslib
- 
--LIBS = -lz -llzma -lbz2 -lm -lpthread
-+LIBS = -lz -llzma -lbz2 -lm -lpthread -lexecinfo
- INCLUDE = -I../src -I../ttmath -I$(VCFLIB_ROOT)/src/ -I$(VCFLIB_ROOT)/smithwaterman/ -I$(VCFLIB_ROOT)/multichoose/ -I$(VCFLIB_ROOT)/filevercmp/ -I$(VCFLIB_ROOT)/fastahack/ -I$(HTSLIB_ROOT) -I$(SEQLIB_ROOT) 
- #INCLUDE = -I../ttmath -I$(BAMTOOLS_ROOT)/src/ -I$(VCFLIB_ROOT)/src/ -I$(TABIX_ROOT)/ -I$(VCFLIB_ROOT)/smithwaterman/ -I$(VCFLIB_ROOT)/multichoose/ -I$(VCFLIB_ROOT)/filevercmp/ -I$(VCFLIB_ROOT)/fastahack/ -I$(HTSLIB_ROOT) -I$(SEQLIB_ROOT) -I$(SEQLIB_ROOT)/htslib
- 
-@@ -46,10 +47,10 @@ gprof:
- .PHONY: all static debug profiling gprof
- 
- $(HTSLIB_ROOT)/libhts.a:
--	cd $(HTSLIB_ROOT) && make
-+	cd $(HTSLIB_ROOT) && ${MAKE}
- 
- $(SEQLIB_ROOT)/src/libseqlib.a:
--	cd $(SEQLIB_ROOT) && ./configure && make 
-+	cd $(SEQLIB_ROOT) && ./configure && ${MAKE} 
- 
- OBJECTS=BedReader.o \
- 		CNV.o \
-@@ -122,7 +123,7 @@ freebayes.o: freebayes.cpp TryCatch.h $(
- 	$(CXX) $(CXXFLAGS) $(INCLUDE) -c freebayes.cpp
- 
- fastlz.o: fastlz.c fastlz.h
--	$(C) $(CFLAGS) $(INCLUDE) -c fastlz.c	
-+	$(CC) $(CFLAGS) $(INCLUDE) -c fastlz.c	
- 
- Parameters.o: Parameters.cpp Parameters.h Version.h
- 	$(CXX) $(CXXFLAGS) $(INCLUDE) -c Parameters.cpp
-@@ -277,5 +278,5 @@ autoversion:
- 
- clean:
- 	rm -rf *.o *.cgh *~ freebayes alleles ../bin/freebayes ../bin/alleles ../vcflib/*.o ../vcflib/tabixpp/*.{o,a} tabix.hpp
--	if [ -d $(BAMTOOLS_ROOT)/build ]; then make -C $(BAMTOOLS_ROOT)/build clean; fi
--	make -C $(VCFLIB_ROOT)/smithwaterman clean
-+	if [ -d $(BAMTOOLS_ROOT)/build ]; then ${MAKE} -C $(BAMTOOLS_ROOT)/build clean; fi
-+	${MAKE} -C $(VCFLIB_ROOT)/smithwaterman clean