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Code Issues Releases Activity

biology/bedtools: Upgrade to 2.27.1

Browse Source 
PR:             227272
Submitted by:   jwb
Approved by:    jrm (mentor)
Differential Revision:  https://reviews.freebsd.org/D15137
This commit is contained in:
Jason W. Bacon 2018-04-19 16:44:59 +00:00
parent e7d0a0751e
commit 8ede5f984e
Notes: svn2git 2021-03-31 03:12:20 +00:00 
svn path=/head/; revision=467783
6 changed files with 36 additions and 54 deletions
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25
biology/bedtools/Makefile
View File

@ -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>

5
biology/bedtools/distinfo
View File

@ -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

44
biology/bedtools/files/patch-Makefile
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@ -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:
@@ -193,7 +193,7 @@ clean:
.PHONY: clean
test: all

11
biology/bedtools/files/patch-src_utils_FileRecordTools_Records_StrandQueue.h
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@ -1,11 +0,0 @@
--- src/utils/FileRecordTools/Records/StrandQueue.h.orig 2015-09-03 04:36:18 UTC
+++ src/utils/FileRecordTools/Records/StrandQueue.h
@@ -30,7 +30,7 @@ public:
private:
// static RecordPtrSortFunctor _recSortFunctor;
- typedef priority_queue<Record *, vector<const Record *>, RecordPtrSortDescFunctor > queueType;
+ typedef priority_queue<Record *, vector<Record *>, RecordPtrSortDescFunctor > queueType;
vector<queueType *> _queues;
static const int NUM_QUEUES = 3;

4
biology/bedtools/pkg-descr
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@ -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,

1
biology/bedtools/pkg-plist
View File

@ -27,6 +27,7 @@ bin/nucBed
bin/pairToBed
bin/pairToPair
bin/randomBed
bin/shiftBed
bin/shuffleBed
bin/slopBed
bin/sortBed