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Index: head/biology/bedtools/Makefile
===================================================================
--- head/biology/bedtools/Makefile
+++ head/biology/bedtools/Makefile
@@ -1,29 +1,30 @@
-# Created by: Scott Cheloha <scottcheloha@gmail.com>
# $FreeBSD$
PORTNAME= bedtools
-PORTVERSION= 2.25.0
DISTVERSIONPREFIX= v
+DISTVERSION= 2.27.1
CATEGORIES= biology
-MASTER_SITES= GITHUB
-MAINTAINER= scottcheloha@gmail.com
-COMMENT= Toolset for genome arithmetic
+MAINTAINER= jwb@FreeBSD.org
+COMMENT= Toolset for genome set arithmetic such as intersect, union
LICENSE= GPLv2
LICENSE_FILE= ${WRKSRC}/LICENSE
+USES= gmake python
USE_GITHUB= yes
GH_ACCOUNT= arq5x
GH_PROJECT= bedtools2
-USES= gmake python
-#NO_ARCH= yes
+pre-build:
+ @${REINPLACE_CMD} -e 's|python|${PYTHON_CMD}|g' ${WRKSRC}/Makefile
+ @${REINPLACE_CMD} -e 's|@\$$(CXX)|$$(CXX)|g' \
+ ${WRKSRC}/*/Makefile \
+ ${WRKSRC}/*/*/Makefile \
+ ${WRKSRC}/*/*/*/Makefile \
+ ${WRKSRC}/*/*/*/*/Makefile
-MAKE_JOBS_UNSAFE= yes
-
-post-patch:
- @${REINPLACE_CMD} -e 's|python|${PYTHON_CMD}|g' \
- ${WRKSRC}/Makefile
+post-install:
+ ${STRIP_CMD} ${STAGEDIR}${PREFIX}/bin/bedtools
.include <bsd.port.mk>
Index: head/biology/bedtools/distinfo
===================================================================
--- head/biology/bedtools/distinfo
+++ head/biology/bedtools/distinfo
@@ -1,2 +1,3 @@
-SHA256 (arq5x-bedtools2-v2.25.0_GH0.tar.gz) = 159122afb9978015f7ec85d7b17739b01415a5738086b20a48147eeefcf08cfb
-SIZE (arq5x-bedtools2-v2.25.0_GH0.tar.gz) = 19586049
+TIMESTAMP = 1519746174
+SHA256 (arq5x-bedtools2-v2.27.1_GH0.tar.gz) = edcac089d84e63a51f85c3c189469daa7d42180272130b046856faad3cf79112
+SIZE (arq5x-bedtools2-v2.27.1_GH0.tar.gz) = 20003119
Index: head/biology/bedtools/files/patch-Makefile
===================================================================
--- head/biology/bedtools/files/patch-Makefile
+++ head/biology/bedtools/files/patch-Makefile
@@ -1,4 +1,4 @@
---- Makefile.orig 2015-11-14 00:48:48 UTC
+--- Makefile.orig 2017-12-14 17:15:02 UTC
+++ Makefile
@@ -4,7 +4,7 @@
# (c) 2009 Aaron Quinlan
@@ -14,38 +14,28 @@
export SRC_DIR = src
export UTIL_DIR = src/utils
-export CXX = g++
-+export CXX = c++
- #ifeq ($(DEBUG),1)
- #export CXXFLAGS = -Wall -O0 -g -fno-inline -fkeep-inline-functions -D_FILE_OFFSET_BITS=64 -fPIC -DDEBUG -D_DEBUG
- #else
++export CXX ?= g++
+ ifeq ($(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 += -Wall -D_FILE_OFFSET_BITS=64 -fPIC $(INCLUDES)
- #endif
- export LIBS = -lz
- export BT_ROOT = src/utils/BamTools/
-@@ -129,20 +129,17 @@ INCLUDES = -I$(SRC_DIR)/utils/bedFile \
- -I$(SRC_DIR)/utils/GenomeFile \
- -I$(SRC_DIR)/utils/RecordOutputMgr \
- -I$(SRC_DIR)/utils/ToolBase \
-- -I$(SRC_DIR)/utils/driver \
--
-+ -I$(SRC_DIR)/utils/driver
++export CXXFLAGS += -D_FILE_OFFSET_BITS=64 -fPIC $(INCLUDES)
+ endif
+ # If the user has specified to do so, tell the compile to use rand() (instead of mt19937).
+@@ -143,8 +143,8 @@ INCLUDES = -I$(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)
++ $(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."
- @python scripts/makeBashScripts.py
- @chmod +x bin/*
- @echo "done."
--
- .PHONY: all
-
-@@ -183,7 +180,7 @@ clean:
+ @echo "- Creating executables for old CLI."
+@@ -193,7 +193,7 @@ clean:
.PHONY: clean
test: all
Index: head/biology/bedtools/files/patch-src_utils_FileRecordTools_Records_StrandQueue.h
===================================================================
--- head/biology/bedtools/files/patch-src_utils_FileRecordTools_Records_StrandQueue.h
+++ head/biology/bedtools/files/patch-src_utils_FileRecordTools_Records_StrandQueue.h
@@ -1,11 +0,0 @@
---- src/utils/FileRecordTools/Records/StrandQueue.h.orig 2015-09-03 04:36:18 UTC
-+++ src/utils/FileRecordTools/Records/StrandQueue.h
-@@ -30,7 +30,7 @@ public:
-
- private:
- // static RecordPtrSortFunctor _recSortFunctor;
-- typedef priority_queue<Record *, vector<const Record *>, RecordPtrSortDescFunctor > queueType;
-+ typedef priority_queue<Record *, vector<Record *>, RecordPtrSortDescFunctor > queueType;
- vector<queueType *> _queues;
- static const int NUM_QUEUES = 3;
-
Index: head/biology/bedtools/pkg-descr
===================================================================
--- head/biology/bedtools/pkg-descr
+++ head/biology/bedtools/pkg-descr
@@ -1,7 +1,7 @@
The bedtools utilities are a suite of tools for performing a wide range of
genomics analysis tasks. The most widely-used of these tools enable genome
-arithmetic, i.e., set theory on the genome. For example, with bedtools one
-can intersect, merge, count, complement, and shuffle genomic intervals from
+arithmetic, i.e., set theory on the genome. For example, with bedtools one can
+intersect, merge, count, complement, and shuffle genomic intervals from
multiple files in common genomic formats such as BAM, BED, GFF/GTF, and VCF.
Although each individual utility is designed to do a relatively simple task,
Index: head/biology/bedtools/pkg-plist
===================================================================
--- head/biology/bedtools/pkg-plist
+++ head/biology/bedtools/pkg-plist
@@ -27,6 +27,7 @@
bin/pairToBed
bin/pairToPair
bin/randomBed
+bin/shiftBed
bin/shuffleBed
bin/slopBed
bin/sortBed

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