Attachment 163109 Details for Bug 204536 – shar(1) of biology/bedtools; Makefile, distinfo, pkg-plist, pkg-descr, and a small patch in files/

shar(1) of biology/bedtools; Makefile, distinfo, pkg-plist, pkg-descr, and a small patch in files/

bedtools.shar (text/plain), 4.74 KB, created by scottcheloha on 2015-11-14 05:22:54 UTC

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Creator: scottcheloha

Created: 2015-11-14 05:22:54 UTC

Size: 4.74 KB

patch

obsolete

># 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
>

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Attachments on bug 204536: 163109