Date: Thu, 19 Apr 2018 16:44:59 +0000 (UTC) From: "Jason W. Bacon" <jwb@FreeBSD.org> To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r467783 - in head/biology/bedtools: . files Message-ID: <201804191644.w3JGixpk002709@repo.freebsd.org>
next in thread | raw e-mail | index | archive | help
Author: jwb Date: Thu Apr 19 16:44:59 2018 New Revision: 467783 URL: https://svnweb.freebsd.org/changeset/ports/467783 Log: biology/bedtools: Upgrade to 2.27.1 PR: 227272 Submitted by: jwb Approved by: jrm (mentor) Differential Revision: https://reviews.freebsd.org/D15137 Deleted: head/biology/bedtools/files/patch-src_utils_FileRecordTools_Records_StrandQueue.h Modified: head/biology/bedtools/Makefile head/biology/bedtools/distinfo head/biology/bedtools/files/patch-Makefile head/biology/bedtools/pkg-descr head/biology/bedtools/pkg-plist Modified: head/biology/bedtools/Makefile ============================================================================== --- head/biology/bedtools/Makefile Thu Apr 19 16:27:51 2018 (r467782) +++ head/biology/bedtools/Makefile Thu Apr 19 16:44:59 2018 (r467783) @@ -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> Modified: head/biology/bedtools/distinfo ============================================================================== --- head/biology/bedtools/distinfo Thu Apr 19 16:27:51 2018 (r467782) +++ head/biology/bedtools/distinfo Thu Apr 19 16:44:59 2018 (r467783) @@ -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 Modified: head/biology/bedtools/files/patch-Makefile ============================================================================== --- head/biology/bedtools/files/patch-Makefile Thu Apr 19 16:27:51 2018 (r467782) +++ head/biology/bedtools/files/patch-Makefile Thu Apr 19 16:44:59 2018 (r467783) @@ -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 Modified: head/biology/bedtools/pkg-descr ============================================================================== --- head/biology/bedtools/pkg-descr Thu Apr 19 16:27:51 2018 (r467782) +++ head/biology/bedtools/pkg-descr Thu Apr 19 16:44:59 2018 (r467783) @@ -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, Modified: head/biology/bedtools/pkg-plist ============================================================================== --- head/biology/bedtools/pkg-plist Thu Apr 19 16:27:51 2018 (r467782) +++ head/biology/bedtools/pkg-plist Thu Apr 19 16:44:59 2018 (r467783) @@ -27,6 +27,7 @@ bin/nucBed bin/pairToBed bin/pairToPair bin/randomBed +bin/shiftBed bin/shuffleBed bin/slopBed bin/sortBed
Want to link to this message? Use this URL: <https://mail-archive.FreeBSD.org/cgi/mid.cgi?201804191644.w3JGixpk002709>