# This is a shell archive.  Save it in a file, remove anything before
# this line, and then unpack it by entering "sh file".  Note, it may
# create directories; files and directories will be owned by you and
# have default permissions.
#
# This archive contains:
#
#	bedtools
#	bedtools/files
#	bedtools/files/patch-Makefile
#	bedtools/pkg-plist
#	bedtools/Makefile
#	bedtools/pkg-descr
#	bedtools/distinfo
#
echo c - bedtools
mkdir -p bedtools > /dev/null 2>&1
echo c - bedtools/files
mkdir -p bedtools/files > /dev/null 2>&1
echo x - bedtools/files/patch-Makefile
sed 's/^X//' >bedtools/files/patch-Makefile << '002cfe5d2cbbdadc6da44c0f8bc5b98c'
X--- Makefile.orig	2015-11-14 00:48:48 UTC
X+++ Makefile
X@@ -4,7 +4,7 @@
X # (c) 2009 Aaron Quinlan
X # ==========================
X 
X-SHELL := /bin/bash -e
X+SHELL := /bin/sh -e
X 
X VERSION_FILE=./src/utils/version/version_git.h
X RELEASED_VERSION_FILE=./src/utils/version/version_release.txt
X@@ -16,11 +16,11 @@ export OBJ_DIR	= obj
X export BIN_DIR	= bin
X export SRC_DIR	= src
X export UTIL_DIR	= src/utils
X-export CXX		= g++
X+export CXX	= c++
X #ifeq ($(DEBUG),1)
X #export CXXFLAGS = -Wall -O0 -g -fno-inline -fkeep-inline-functions -D_FILE_OFFSET_BITS=64 -fPIC -DDEBUG -D_DEBUG
X #else
X-export CXXFLAGS = -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC $(INCLUDES)
X+export CXXFLAGS += -Wall -D_FILE_OFFSET_BITS=64 -fPIC $(INCLUDES)
X #endif
X export LIBS		= -lz
X export BT_ROOT  = src/utils/BamTools/
X@@ -129,20 +129,17 @@ INCLUDES =	-I$(SRC_DIR)/utils/bedFile \
X 				-I$(SRC_DIR)/utils/GenomeFile \
X 				-I$(SRC_DIR)/utils/RecordOutputMgr \
X 				-I$(SRC_DIR)/utils/ToolBase \
X-				-I$(SRC_DIR)/utils/driver \
X-				
X+				-I$(SRC_DIR)/utils/driver
X 
X all: print_banner $(OBJ_DIR) $(BIN_DIR) autoversion $(UTIL_SUBDIRS) $(SUBDIRS)
X 	@echo "- Building main bedtools binary."
X 	@$(CXX) $(CXXFLAGS) $(CPPFLAGS) -c src/bedtools.cpp -o obj/bedtools.o $(INCLUDES)
X 	@$(CXX) $(CXXFLAGS) $(CPPFLAGS) -o $(BIN_DIR)/bedtools $(BUILT_OBJECTS) -L$(UTIL_DIR)/BamTools/lib/ -lbamtools $(LIBS) $(LDFLAGS) $(INCLUDES)
X 	@echo "done."
X-	
X 	@echo "- Creating executables for old CLI."
X 	@python scripts/makeBashScripts.py
X 	@chmod +x bin/*
X 	@echo "done."
X-	
X 
X .PHONY: all
X 
X@@ -183,7 +180,7 @@ clean:
X .PHONY: clean
X 
X test: all
X-	@cd test; bash test.sh
X+	@cd test; $(SHELL) test.sh
X 
X .PHONY: test
X 
002cfe5d2cbbdadc6da44c0f8bc5b98c
echo x - bedtools/pkg-plist
sed 's/^X//' >bedtools/pkg-plist << '8ea852f67de582d36688f5dbfc7cf906'
Xbin/annotateBed
Xbin/bamToBed
Xbin/bamToFastq
Xbin/bed12ToBed6
Xbin/bedToBam
Xbin/bedToIgv
Xbin/bedpeToBam
Xbin/bedtools
Xbin/closestBed
Xbin/clusterBed
Xbin/complementBed
Xbin/coverageBed
Xbin/expandCols
Xbin/fastaFromBed
Xbin/flankBed
Xbin/genomeCoverageBed
Xbin/getOverlap
Xbin/groupBy
Xbin/intersectBed
Xbin/linksBed
Xbin/mapBed
Xbin/maskFastaFromBed
Xbin/mergeBed
Xbin/multiBamCov
Xbin/multiIntersectBed
Xbin/nucBed
Xbin/pairToBed
Xbin/pairToPair
Xbin/randomBed
Xbin/shuffleBed
Xbin/slopBed
Xbin/sortBed
Xbin/subtractBed
Xbin/tagBam
Xbin/unionBedGraphs
Xbin/windowBed
Xbin/windowMaker
8ea852f67de582d36688f5dbfc7cf906
echo x - bedtools/Makefile
sed 's/^X//' >bedtools/Makefile << 'ac5695028118ce608654239112855531'
X# Created by: Scott Cheloha <scottcheloha@gmail.com>
X# $FreeBSD$
X
XPORTNAME=	bedtools
XPORTVERSION=	2.25.0
XCATEGORIES=	biology
XMASTER_SITES=	GITHUB
X
XMAINTAINER=	scottcheloha@gmail.com
XCOMMENT=	Toolset for genome arithmetic
X
XLICENSE=	GPLv2
XLICENSE_FILE=	${WRKSRC}/LICENSE
X
XUSE_GITHUB=	yes
XGH_ACCOUNT=	arq5x
XGH_PROJECT=	bedtools2
XGH_TAGNAME=	v2.25.0
X
XUSES=		gmake
XNO_ARCH=	yes
XBUILD_DEPENDS=	python:${PORTSDIR}/lang/python
X
X.include <bsd.port.mk>
ac5695028118ce608654239112855531
echo x - bedtools/pkg-descr
sed 's/^X//' >bedtools/pkg-descr << '2497548a4f1763c5b015d9711c4e28c9'
XThe bedtools utilities are a suite of tools for performing a wide range of
Xgenomics analysis tasks.  The most widely-used of these tools enable genome
Xarithmetic, i.e., set theory on the genome.  For example, with bedtools one
Xcan intersect, merge, count, complement, and shuffle genomic intervals from
Xmultiple files in common genomic formats such as BAM, BED, GFF/GTF, and VCF.
X
XAlthough each individual utility is designed to do a relatively simple task,
Xe.g., intersect two interval files, more sophisticated analyses can be
Xconducted by stringing together multiple bedtools operations on the command
Xline or in shell scripts.
X
XWWW: http://bedtools.readthedocs.org/
2497548a4f1763c5b015d9711c4e28c9
echo x - bedtools/distinfo
sed 's/^X//' >bedtools/distinfo << '879a8bb032e8809c752d856925dce9de'
XSHA256 (arq5x-bedtools2-2.25.0-v2.25.0_GH0.tar.gz) = 159122afb9978015f7ec85d7b17739b01415a5738086b20a48147eeefcf08cfb
XSIZE (arq5x-bedtools2-2.25.0-v2.25.0_GH0.tar.gz) = 19586049
879a8bb032e8809c752d856925dce9de
exit