diff options
Diffstat (limited to 'sci-biology/bedtools/files/bedtools-2.29.2-buildsystem.patch')
| -rw-r--r-- | sci-biology/bedtools/files/bedtools-2.29.2-buildsystem.patch | 82 |
1 files changed, 82 insertions, 0 deletions
diff --git a/sci-biology/bedtools/files/bedtools-2.29.2-buildsystem.patch b/sci-biology/bedtools/files/bedtools-2.29.2-buildsystem.patch new file mode 100644 index 000000000000..573e88993bc9 --- /dev/null +++ b/sci-biology/bedtools/files/bedtools-2.29.2-buildsystem.patch @@ -0,0 +1,82 @@ +--- a/Makefile ++++ b/Makefile +@@ -4,44 +4,29 @@ + # (c) 2009 Aaron Quinlan + # ========================== + +-SHELL := /bin/bash -e ++SHELL := bash -e + + VERSION_FILE=./src/utils/version/version_git.h + RELEASED_VERSION_FILE=./src/utils/version/version_release.txt + + + # define our object and binary directories +-ifeq ($(VERBOSE),1) + CCPREFIX = +-else +-CCPREFIX = @ +-endif + + OBJ_DIR = obj + BIN_DIR = bin + SRC_DIR = src + +-CXX = g++ +- +-ifeq ($(DEBUG),1) +-BT_CPPFLAGS = -DDEBUG -D_DEBUG -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API $(INCLUDES) +-BT_CXXFLAGS = -Wconversion -Wall -Wextra -g -O0 +-else + BT_CPPFLAGS = -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API $(INCLUDES) +-BT_CXXFLAGS = -g -Wall -O2 +-endif ++BT_CXXFLAGS = -Wall + + # If the user has specified to do so, tell the compile to use rand() (instead of mt19937). +-ifeq ($(USE_RAND),1) +-BT_CXXFLAGS += -DUSE_RAND +-else + BT_CXXFLAGS += -std=c++11 +-endif + + BT_LDFLAGS = + BT_LIBS = -lz -lm -lbz2 -llzma -lpthread + +-prefix ?= /usr/local ++prefix = $(EPREFIX)/usr + + SUBDIRS = $(SRC_DIR)/annotateBed \ + $(SRC_DIR)/bamToBed \ +@@ -204,7 +189,7 @@ + + # make the "obj/" and "bin/" directories, if they don't exist + $(OBJ_DIR) $(BIN_DIR): +- @mkdir -p $@ ++ mkdir -p $@ + + + # Usually HTSlib's configure script has not been used (detected via config.mk +--- a/src/utils/htslib/Makefile ++++ b/src/utils/htslib/Makefile +@@ -22,20 +22,13 @@ + # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER + # DEALINGS IN THE SOFTWARE. + +-CC = gcc +-AR = ar +-RANLIB = ranlib +- + # Default libraries to link if configure is not used + htslib_default_libs = -lz -lm -lbz2 -llzma + +-CPPFLAGS = + # TODO: probably update cram code to make it compile cleanly with -Wc++-compat + # For testing strict C99 support add -std=c99 -D_XOPEN_SOURCE=600 + #CFLAGS = -g -Wall -O2 -pedantic -std=c99 -D_XOPEN_SOURCE=600 -D__FUNCTION__=__func__ +-CFLAGS = -g -Wall -O2 + EXTRA_CFLAGS_PIC = -fpic +-LDFLAGS = + LIBS = $(htslib_default_libs) + + prefix = /usr/local |