From owner-svn-ports-all@freebsd.org Tue Jan 19 08:56:36 2016 Return-Path: Delivered-To: svn-ports-all@mailman.ysv.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2001:1900:2254:206a::19:1]) by mailman.ysv.freebsd.org (Postfix) with ESMTP id 6921FA8789B; Tue, 19 Jan 2016 08:56:36 +0000 (UTC) (envelope-from wen@FreeBSD.org) Received: from repo.freebsd.org (repo.freebsd.org [IPv6:2610:1c1:1:6068::e6a:0]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (Client did not present a certificate) by mx1.freebsd.org (Postfix) with ESMTPS id 3FF581AE4; Tue, 19 Jan 2016 08:56:36 +0000 (UTC) (envelope-from wen@FreeBSD.org) Received: from repo.freebsd.org ([127.0.1.37]) by repo.freebsd.org (8.15.2/8.15.2) with ESMTP id u0J8uZCt017343; Tue, 19 Jan 2016 08:56:35 GMT (envelope-from wen@FreeBSD.org) Received: (from wen@localhost) by repo.freebsd.org (8.15.2/8.15.2/Submit) id u0J8uYum017337; Tue, 19 Jan 2016 08:56:34 GMT (envelope-from wen@FreeBSD.org) Message-Id: <201601190856.u0J8uYum017337@repo.freebsd.org> X-Authentication-Warning: repo.freebsd.org: wen set sender to wen@FreeBSD.org using -f From: Wen Heping Date: Tue, 19 Jan 2016 08:56:34 +0000 (UTC) To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r406676 - in head/biology: . bedtools bedtools/files X-SVN-Group: ports-head MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit X-BeenThere: svn-ports-all@freebsd.org X-Mailman-Version: 2.1.20 Precedence: list List-Id: SVN commit messages for the ports tree List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Tue, 19 Jan 2016 08:56:36 -0000 Author: wen Date: Tue Jan 19 08:56:34 2016 New Revision: 406676 URL: https://svnweb.freebsd.org/changeset/ports/406676 Log: 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 Added: head/biology/bedtools/ head/biology/bedtools/Makefile (contents, props changed) head/biology/bedtools/distinfo (contents, props changed) head/biology/bedtools/files/ head/biology/bedtools/files/patch-Makefile (contents, props changed) head/biology/bedtools/pkg-descr (contents, props changed) head/biology/bedtools/pkg-plist (contents, props changed) Modified: head/biology/Makefile Modified: head/biology/Makefile ============================================================================== --- head/biology/Makefile Tue Jan 19 08:38:47 2016 (r406675) +++ head/biology/Makefile Tue Jan 19 08:56:34 2016 (r406676) @@ -8,6 +8,7 @@ SUBDIR += avida SUBDIR += babel SUBDIR += bcftools + SUBDIR += bedtools SUBDIR += biococoa SUBDIR += biojava SUBDIR += blat Added: head/biology/bedtools/Makefile ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/bedtools/Makefile Tue Jan 19 08:56:34 2016 (r406676) @@ -0,0 +1,27 @@ +# Created by: Scott Cheloha +# $FreeBSD$ + +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' \ + ${WRKSRC}/Makefile + +.include Added: head/biology/bedtools/distinfo ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/bedtools/distinfo Tue Jan 19 08:56:34 2016 (r406676) @@ -0,0 +1,2 @@ +SHA256 (arq5x-bedtools2-v2.25.0_GH0.tar.gz) = 159122afb9978015f7ec85d7b17739b01415a5738086b20a48147eeefcf08cfb +SIZE (arq5x-bedtools2-v2.25.0_GH0.tar.gz) = 19586049 Added: head/biology/bedtools/files/patch-Makefile ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/bedtools/files/patch-Makefile Tue Jan 19 08:56:34 2016 (r406676) @@ -0,0 +1,56 @@ +--- Makefile.orig 2015-11-14 00:48:48 UTC ++++ Makefile +@@ -4,7 +4,7 @@ + # (c) 2009 Aaron Quinlan + # ========================== + +-SHELL := /bin/bash -e ++SHELL := /bin/sh -e + + VERSION_FILE=./src/utils/version/version_git.h + RELEASED_VERSION_FILE=./src/utils/version/version_release.txt +@@ -16,11 +16,11 @@ export OBJ_DIR = obj + export BIN_DIR = bin + export SRC_DIR = src + export UTIL_DIR = src/utils +-export CXX = g++ ++export CXX = c++ + #ifeq ($(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 + Added: head/biology/bedtools/pkg-descr ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/bedtools/pkg-descr Tue Jan 19 08:56:34 2016 (r406676) @@ -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/ Added: head/biology/bedtools/pkg-plist ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/bedtools/pkg-plist Tue Jan 19 08:56:34 2016 (r406676) @@ -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