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
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,
e.g., intersect two interval files, more sophisticated analyses can be
conducted by stringing together multiple bedtools operations on the command
line or in shell scripts.

WWW: http://bedtools.readthedocs.org/

PR:		204536
Submitted by:	scottcheloha@gmail.com

6 files changed, 135 insertions, 0 deletions

diff --git a/biology/Makefile b/biology/Makefile
index 9630fba8eda8..ecc99f382bfa 100644
--- a/biology/Makefile
+++ b/biology/Makefile
@@ -8,6 +8,7 @@
     SUBDIR += avida
     SUBDIR += babel
     SUBDIR += bcftools
+    SUBDIR += bedtools
     SUBDIR += biococoa
     SUBDIR += biojava
     SUBDIR += blat
diff --git a/biology/bedtools/Makefile b/biology/bedtools/Makefile
new file mode 100644
index 000000000000..8e57fffc3f39
--- /dev/null
+++ b/biology/bedtools/Makefile
@@ -0,0 +1,27 @@
+# Created by: Scott Cheloha <scottcheloha@gmail.com>
+# $FreeBSD$
+
+PORTNAME=	bedtools
+PORTVERSION=	2.25.0
+DISTVERSIONPREFIX=	v
+CATEGORIES=	biology
+MASTER_SITES=	GITHUB
+
+MAINTAINER=	scottcheloha@gmail.com
+COMMENT=	Toolset for genome arithmetic
+
+LICENSE=	GPLv2
+LICENSE_FILE=	${WRKSRC}/LICENSE
+
+USE_GITHUB=	yes
+GH_ACCOUNT=	arq5x
+GH_PROJECT=	bedtools2
+
+USES=		gmake python
+#NO_ARCH=	yes
+
+post-patch:
+	@${REINPLACE_CMD} -e 's|python|${PYTHON_CMD}|g' \
+		${WRKSRC}/Makefile
+
+.include <bsd.port.mk>
diff --git a/biology/bedtools/distinfo b/biology/bedtools/distinfo
new file mode 100644
index 000000000000..49d6b6491c63
--- /dev/null
+++ b/biology/bedtools/distinfo
@@ -0,0 +1,2 @@
+SHA256 (arq5x-bedtools2-v2.25.0_GH0.tar.gz) = 159122afb9978015f7ec85d7b17739b01415a5738086b20a48147eeefcf08cfb
+SIZE (arq5x-bedtools2-v2.25.0_GH0.tar.gz) = 19586049
diff --git a/biology/bedtools/files/patch-Makefile b/biology/bedtools/files/patch-Makefile
new file mode 100644
index 000000000000..3c479bc9f999
--- /dev/null
+++ b/biology/bedtools/files/patch-Makefile
@@ -0,0 +1,56 @@
+--- Makefile.orig	2015-11-14 00:48:48 UTC
++++ Makefile
+@@ -4,7 +4,7 @@
+ # (c) 2009 Aaron Quinlan
+ # ==========================
+ 
+-SHELL := /bin/bash -e
++SHELL := /bin/sh -e
+ 
+ VERSION_FILE=./src/utils/version/version_git.h
+ RELEASED_VERSION_FILE=./src/utils/version/version_release.txt
+@@ -16,11 +16,11 @@ export OBJ_DIR	= obj
+ export BIN_DIR	= bin
+ export SRC_DIR	= src
+ export UTIL_DIR	= src/utils
+-export CXX		= g++
++export CXX	= c++
+ #ifeq ($(DEBUG),1)
+ #export CXXFLAGS = -Wall -O0 -g -fno-inline -fkeep-inline-functions -D_FILE_OFFSET_BITS=64 -fPIC -DDEBUG -D_DEBUG
+ #else
+-export 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
+ 
+ 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)
+ 	@echo "done."
+-	
+ 	@echo "- Creating executables for old CLI."
+ 	@python scripts/makeBashScripts.py
+ 	@chmod +x bin/*
+ 	@echo "done."
+-	
+ 
+ .PHONY: all
+ 
+@@ -183,7 +180,7 @@ clean:
+ .PHONY: clean
+ 
+ test: all
+-	@cd test; bash test.sh
++	@cd test; $(SHELL) test.sh
+ 
+ .PHONY: test
+ 
diff --git a/biology/bedtools/pkg-descr b/biology/bedtools/pkg-descr
new file mode 100644
index 000000000000..6eb2df9dab04
--- /dev/null
+++ b/biology/bedtools/pkg-descr
@@ -0,0 +1,12 @@
+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
+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,
+e.g., intersect two interval files, more sophisticated analyses can be
+conducted by stringing together multiple bedtools operations on the command
+line or in shell scripts.
+
+WWW: http://bedtools.readthedocs.org/
diff --git a/biology/bedtools/pkg-plist b/biology/bedtools/pkg-plist
new file mode 100644
index 000000000000..3ad56455ec57
--- /dev/null
+++ b/biology/bedtools/pkg-plist
@@ -0,0 +1,37 @@
+bin/annotateBed
+bin/bamToBed
+bin/bamToFastq
+bin/bed12ToBed6
+bin/bedToBam
+bin/bedToIgv
+bin/bedpeToBam
+bin/bedtools
+bin/closestBed
+bin/clusterBed
+bin/complementBed
+bin/coverageBed
+bin/expandCols
+bin/fastaFromBed
+bin/flankBed
+bin/genomeCoverageBed
+bin/getOverlap
+bin/groupBy
+bin/intersectBed
+bin/linksBed
+bin/mapBed
+bin/maskFastaFromBed
+bin/mergeBed
+bin/multiBamCov
+bin/multiIntersectBed
+bin/nucBed
+bin/pairToBed
+bin/pairToPair
+bin/randomBed
+bin/shuffleBed
+bin/slopBed
+bin/sortBed
+bin/subtractBed
+bin/tagBam
+bin/unionBedGraphs
+bin/windowBed
+bin/windowMaker