5 files changed, 64 insertions, 49 deletions

diff --git a/biology/bedtools/Makefile b/biology/bedtools/Makefile
index 7595ab5a82de..19e0173cac27 100644
--- a/biology/bedtools/Makefile
+++ b/biology/bedtools/Makefile
@@ -1,10 +1,9 @@
 # $FreeBSD$
 
-PORTNAME=	bedtools
+PORTNAME=		bedtools
 DISTVERSIONPREFIX=	v
-DISTVERSION=	2.27.1
-PORTREVISION=	3
-CATEGORIES=	biology
+DISTVERSION=		2.29.0
+CATEGORIES=		biology
 
 MAINTAINER=	jwb@FreeBSD.org
 COMMENT=	Toolset for genome set arithmetic such as intersect, union
@@ -12,6 +11,8 @@ COMMENT=	Toolset for genome set arithmetic such as intersect, union
 LICENSE=	GPLv2
 LICENSE_FILE=	${WRKSRC}/LICENSE
 
+TEST_DEPENDS=	bash:shells/bash
+
 USES=		compiler:c++11-lang gmake python
 USE_GITHUB=	yes
 GH_ACCOUNT=	arq5x
@@ -22,15 +23,17 @@ post-extract:
 	@${MV} ${WRKSRC}/src/utils/gzstream/version \
 		${WRKSRC}/src/utils/gzstream/version.txt
 
-pre-build:
+pre-configure:
 	@${REINPLACE_CMD} -e 's|python|${PYTHON_CMD}|g' ${WRKSRC}/Makefile
 	@${REINPLACE_CMD} -e 's|@\$$(CXX)|$$(CXX)|g' \
 		${WRKSRC}/*/Makefile \
 		${WRKSRC}/*/*/Makefile \
-		${WRKSRC}/*/*/*/Makefile \
-		${WRKSRC}/*/*/*/*/Makefile
+		${WRKSRC}/*/*/*/Makefile
 
 post-install:
 	${STRIP_CMD} ${STAGEDIR}${PREFIX}/bin/bedtools
 
+do-test:
+	(cd ${WRKSRC}/test && bash test.sh)
+
 .include <bsd.port.mk>
diff --git a/biology/bedtools/distinfo b/biology/bedtools/distinfo
index bd752c979d56..17636136ba72 100644
--- a/biology/bedtools/distinfo
+++ b/biology/bedtools/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1519746174
-SHA256 (arq5x-bedtools2-v2.27.1_GH0.tar.gz) = edcac089d84e63a51f85c3c189469daa7d42180272130b046856faad3cf79112
-SIZE (arq5x-bedtools2-v2.27.1_GH0.tar.gz) = 20003119
+TIMESTAMP = 1567891084
+SHA256 (arq5x-bedtools2-v2.29.0_GH0.tar.gz) = 8a13b7ec93a2dc960616268d8009f6061bec5a32b8a38d5734f80e851bb8ed1e
+SIZE (arq5x-bedtools2-v2.29.0_GH0.tar.gz) = 20635364
diff --git a/biology/bedtools/files/patch-Makefile b/biology/bedtools/files/patch-Makefile
index 6a947277fe1c..16159fa81527 100644
--- a/biology/bedtools/files/patch-Makefile
+++ b/biology/bedtools/files/patch-Makefile
@@ -1,4 +1,4 @@
---- Makefile.orig	2017-12-14 17:15:02 UTC
+--- Makefile.orig	2019-09-07 21:14:56 UTC
 +++ Makefile
 @@ -4,7 +4,7 @@
  # (c) 2009 Aaron Quinlan
@@ -9,42 +9,25 @@
  
  VERSION_FILE=./src/utils/version/version_git.h
  RELEASED_VERSION_FILE=./src/utils/version/version_release.txt
-@@ -16,11 +16,11 @@ export OBJ_DIR	= obj
- export BIN_DIR	= bin
- export SRC_DIR	= src
- export UTIL_DIR	= src/utils
--export CXX		= g++
-+export CXX		?= g++
- ifeq ($(DEBUG),1)
--export CXXFLAGS = -Wall -Wextra -DDEBUG -D_DEBUG -g -O0 -D_FILE_OFFSET_BITS=64 -fPIC $(INCLUDES)
-+export CXXFLAGS += -Wall -Wextra -DDEBUG -D_DEBUG -g -O0 -D_FILE_OFFSET_BITS=64 -fPIC $(INCLUDES)
- else
--export CXXFLAGS = -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC $(INCLUDES)
-+export CXXFLAGS += -D_FILE_OFFSET_BITS=64 -fPIC $(INCLUDES)
- endif
+@@ -20,7 +20,7 @@ OBJ_DIR	= obj
+ BIN_DIR	= bin
+ SRC_DIR	= src
+ 
+-CXX     = g++
++CXX     ?= g++
  
- # If the user has specified to do so, tell the compile to use rand() (instead of mt19937).
-@@ -33,7 +33,7 @@ endif 
- export LIBS		= -lz
- export BT_ROOT  = src/utils/BamTools/
+ ifeq ($(DEBUG),1)
+ BT_CPPFLAGS = -DDEBUG -D_DEBUG -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API $(INCLUDES)
+@@ -40,7 +40,7 @@ endif
+ BT_LDFLAGS =
+ BT_LIBS    = -lz -lm -lbz2 -llzma -lpthread
  
 -prefix ?= /usr/local
 +PREFIX ?= /usr/local
  
  SUBDIRS = $(SRC_DIR)/annotateBed \
  		  $(SRC_DIR)/bamToBed \
-@@ -143,8 +143,8 @@ INCLUDES =	-I$(SRC_DIR)/utils/bedFile \
- 
- all: print_banner $(OBJ_DIR) $(BIN_DIR) autoversion $(UTIL_SUBDIRS) $(SUBDIRS)
- 	@echo "- Building main bedtools binary."
--	@$(CXX) $(CXXFLAGS) $(CPPFLAGS) -c src/bedtools.cpp -o obj/bedtools.o $(INCLUDES)
--	@$(CXX) $(CXXFLAGS) $(CPPFLAGS) -o $(BIN_DIR)/bedtools $(BUILT_OBJECTS) -L$(UTIL_DIR)/BamTools/lib/ -lbamtools $(LIBS) $(LDFLAGS) $(INCLUDES)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) -c src/bedtools.cpp -o obj/bedtools.o $(INCLUDES)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) -o $(BIN_DIR)/bedtools $(BUILT_OBJECTS) -L$(UTIL_DIR)/BamTools/lib/ -lbamtools $(LIBS) $(LDFLAGS) $(INCLUDES)
- 	@echo "done."
- 
- 	@echo "- Creating executables for old CLI."
-@@ -156,9 +156,9 @@ all: print_banner $(OBJ_DIR) $(BIN_DIR) 
+@@ -183,9 +183,9 @@ $(BIN_DIR)/intersectBed: | $(BIN_DIR)
  .PHONY: all
  
  install: all
@@ -56,12 +39,3 @@
  	done
  
  print_banner:
-@@ -193,7 +193,7 @@ clean:
- .PHONY: clean
- 
- test: all
--	@cd test; bash test.sh
-+	@cd test; $(SHELL) test.sh
- 
- .PHONY: test
- 
diff --git a/biology/bedtools/files/patch-src_utils_Contexts_ContextBase.h b/biology/bedtools/files/patch-src_utils_Contexts_ContextBase.h
new file mode 100644
index 000000000000..89f21e42296f
--- /dev/null
+++ b/biology/bedtools/files/patch-src_utils_Contexts_ContextBase.h
@@ -0,0 +1,11 @@
+--- src/utils/Contexts/ContextBase.h.orig	2019-03-25 18:03:45 UTC
++++ src/utils/Contexts/ContextBase.h
+@@ -44,7 +44,7 @@ public:
+ 	FileRecordMgr *getFile(int fileIdx) { return _files[fileIdx]; }
+ 	void setProgram(PROGRAM_TYPE program) { _program = program; }
+ 
+-	void addInputFile(const string &inputFile) { _fileNames.push_back(inputFile); }
++	void addInputFile(const string &inputFile) { _fileNames.push_back(inputFile); cerr << "Adding " << inputFile << endl; }
+ 
+ 	int getNumInputFiles() const { return _fileNames.size(); }
+ 	const string &getInputFileName(int fileNum) const { return _fileNames[fileNum]; }
diff --git a/biology/bedtools/files/patch-src_utils_htslib_Makefile b/biology/bedtools/files/patch-src_utils_htslib_Makefile
new file mode 100644
index 000000000000..7ca62f5eb33a
--- /dev/null
+++ b/biology/bedtools/files/patch-src_utils_htslib_Makefile
@@ -0,0 +1,27 @@
+--- src/utils/htslib/Makefile.orig	2019-03-25 03:58:18 UTC
++++ src/utils/htslib/Makefile
+@@ -22,9 +22,9 @@
+ # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+ # DEALINGS IN THE SOFTWARE.
+ 
+-CC     = gcc
+-AR     = ar
+-RANLIB = ranlib
++CC     ?= gcc
++AR     ?= ar
++RANLIB ?= ranlib
+ 
+ # Default libraries to link if configure is not used
+ htslib_default_libs = -lz -lm -lbz2 -llzma
+@@ -33,9 +33,9 @@ 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
++CFLAGS   ?= -g -Wall -O2
+ EXTRA_CFLAGS_PIC = -fpic
+-LDFLAGS  =
++LDFLAGS  ?=
+ LIBS     = $(htslib_default_libs)
+ 
+ prefix      = /usr/local