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biology/fastp: Update to 0.23.1

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Performance improvements, more reproducible output
Fix seg fault when running with no args
This commit is contained in:
Jason W. Bacon 2021-10-20 11:35:11 -05:00
parent 3146c8ed7f
commit f6c6c5a379
4 changed files with 56 additions and 21 deletions
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7
biology/fastp/Makefile
View file

@ -1,6 +1,6 @@
PORTNAME= fastp PORTNAME= fastp
DISTVERSIONPREFIX= v DISTVERSIONPREFIX= v
DISTVERSION= 0.22.0 DISTVERSION= 0.23.1
CATEGORIES= biology CATEGORIES= biology
MAINTAINER= jwb@FreeBSD.org MAINTAINER= jwb@FreeBSD.org
@ -9,7 +9,10 @@ COMMENT= Ultra-fast all-in-one FASTQ preprocessor
LICENSE= MIT LICENSE= MIT
LICENSE_FILE= ${WRKSRC}/LICENSE LICENSE_FILE= ${WRKSRC}/LICENSE
USES= compiler:c++11-lang gmake LIB_DEPENDS= libdeflate.so:archivers/libdeflate \
libisal.so:devel/isa-l
USES= compiler:c++11-lang gmake localbase:ldflags
USE_GITHUB= yes USE_GITHUB= yes
GH_ACCOUNT= OpenGene GH_ACCOUNT= OpenGene

6
biology/fastp/distinfo
View file

@ -1,3 +1,3 @@
TIMESTAMP = 1630006835 TIMESTAMP = 1634739193
SHA256 (OpenGene-fastp-v0.22.0_GH0.tar.gz) = a7ef81cc39daed7ac6bfc254697345c448095539e1b5b45f3a8ab286098be456 SHA256 (OpenGene-fastp-v0.23.1_GH0.tar.gz) = 32cb16ea1199a5f722d3c5caa24d1aaace4b24f6efa0fd774f227d8a80ebb8f3
SIZE (OpenGene-fastp-v0.22.0_GH0.tar.gz) = 141257 SIZE (OpenGene-fastp-v0.23.1_GH0.tar.gz) = 163190

47
biology/fastp/files/patch-Makefile
View file

@ -1,42 +1,57 @@
--- Makefile.orig 2020-04-08 07:26:52 UTC --- Makefile.orig 2021-10-19 02:19:29 UTC
+++ Makefile +++ Makefile
@@ -3,9 +3,11 @@ DIR_SRC := ./src @@ -2,11 +2,13 @@ DIR_INC := ./inc
DIR_SRC := ./src
DIR_OBJ := ./obj DIR_OBJ := ./obj
PREFIX ?= /usr/local -PREFIX ?= /usr/local
+DESTDIR ?= -BINDIR ?= $(PREFIX)/bin
BINDIR ?= $(PREFIX)/bin -INCLUDE_DIRS ?=
INCLUDE_DIRS ?= -LIBRARY_DIRS ?=
LIBRARY_DIRS ?= +PREFIX ?= /usr/local
+STRIP_CMD ?= strip +BINDIR ?= $(PREFIX)/bin
+INCLUDE_DIRS ?=
+LIBRARY_DIRS ?=
+STRIP ?= strip
+
SRC := $(wildcard ${DIR_SRC}/*.cpp) SRC := $(wildcard ${DIR_SRC}/*.cpp)
OBJ := $(patsubst %.cpp,${DIR_OBJ}/%.o,$(notdir ${SRC})) OBJ := $(patsubst %.cpp,${DIR_OBJ}/%.o,$(notdir ${SRC}))
@@ -15,13 +17,14 @@ TARGET := fastp
@@ -15,15 +17,19 @@ TARGET := fastp
BIN_TARGET := ${TARGET} BIN_TARGET := ${TARGET}
CXX ?= g++ CXX ?= g++
-CXXFLAGS := -std=c++11 -g -O3 -I${DIR_INC} $(foreach includedir,$(INCLUDE_DIRS),-I$(includedir)) ${CXXFLAGS} -CXXFLAGS := -std=c++11 -pthread -g -O3 -I${DIR_INC} $(foreach includedir,$(INCLUDE_DIRS),-I$(includedir)) ${CXXFLAGS}
+# Optional flags that the user can override by setting CXXFLAGS in the
+# env or make argument
+CXXFLAGS ?= -g -O3 +CXXFLAGS ?= -g -O3
+# Required flags
+CXXFLAGS += -std=c++11 -I${DIR_INC} $(foreach includedir,$(INCLUDE_DIRS),-I$(includedir)) +CXXFLAGS += -std=c++11 -I${DIR_INC} $(foreach includedir,$(INCLUDE_DIRS),-I$(includedir))
LIBS := -lz -lpthread LIBS := -lisal -ldeflate -lpthread
STATIC_FLAGS := -static -Wl,--no-as-needed -pthread
-LD_FLAGS := $(foreach librarydir,$(LIBRARY_DIRS),-L$(librarydir)) $(LIBS) $(LD_FLAGS) -LD_FLAGS := $(foreach librarydir,$(LIBRARY_DIRS),-L$(librarydir)) $(LIBS) $(LD_FLAGS)
+# Append required flags to standard LDFLAGS from env
+LDFLAGS += $(foreach librarydir,$(LIBRARY_DIRS),-L$(librarydir)) $(LIBS) +LDFLAGS += $(foreach librarydir,$(LIBRARY_DIRS),-L$(librarydir)) $(LIBS)
STATIC_LD_FLAGS := $(foreach librarydir,$(LIBRARY_DIRS),-L$(librarydir)) $(STATIC_FLAGS) $(LIBS) $(STATIC_LD_FLAGS)
-
${BIN_TARGET}:${OBJ} ${BIN_TARGET}:${OBJ}
- $(CXX) $(OBJ) -o $@ $(LD_FLAGS) - $(CXX) $(OBJ) -o $@ $(LD_FLAGS)
+ $(CXX) $(OBJ) -o $@ $(LDFLAGS) + $(CXX) $(OBJ) -o $@ $(LDFLAGS)
${DIR_OBJ}/%.o:${DIR_SRC}/%.cpp make_obj_dir static:${OBJ}
$(CXX) -c $< -o $@ $(CXXFLAGS) $(CXX) $(OBJ) -o ${BIN_TARGET} $(STATIC_LD_FLAGS)
@@ -38,5 +41,8 @@ make_obj_dir: @@ -49,6 +55,11 @@ make_obj_dir:
mkdir $(DIR_OBJ) ; \
fi fi
+# Respect DESTDIR for staged installs (used by most package managers)
install: install:
- install $(TARGET) $(BINDIR)/$(TARGET) - install $(TARGET) $(BINDIR)/$(TARGET)
+ install $(TARGET) $(DESTDIR)$(BINDIR)/$(TARGET) + install $(TARGET) $(DESTDIR)$(BINDIR)/$(TARGET)
@echo "Installed." @echo "Installed."
+ +
+# Many package managers use install-strip target if debugging is not enabled
+install-strip: install +install-strip: install
+ $(STRIP_CMD) $(DESTDIR)$(BINDIR)/$(TARGET) + $(STRIP) $(DESTDIR)$(BINDIR)/$(TARGET)

17
biology/fastp/files/patch-src_main.cpp Normal file
View file

@ -0,0 +1,17 @@
--- src/main.cpp.orig 2021-10-19 02:19:29 UTC
+++ src/main.cpp
@@ -1,4 +1,5 @@
#include <stdio.h>
+#include <sysexits.h>
#include "fastqreader.h"
#include "unittest.h"
#include <time.h>
@@ -18,7 +19,7 @@ int main(int argc, char* argv[]){
if(argc == 1) {
cerr << "fastp: an ultra-fast all-in-one FASTQ preprocessor" << endl << "version " << FASTP_VER << endl;
//cerr << "fastp --help to see the help"<<endl;
- //return 0;
+ return EX_USAGE;
}
if (argc == 2 && strcmp(argv[1], "test")==0){
UnitTest tester;