biology/fastp: Update to 0.22.0
Adds deduplication subcommand Changes: https://github.com/OpenGene/fastp/releases Holding off on 0.23, which depends on the non-portable Intel isa-l, which does not build on Darwin aarch64
This commit is contained in:
bacon
parent
ed09afa314
commit
d2a9082f53
|
|
@ -1,6 +1,8 @@
|
|||
# $NetBSD: Makefile,v 1.2 2020/05/25 05:18:35 rillig Exp $
|
||||
# $NetBSD: Makefile,v 1.3 2023/06/01 13:03:53 bacon Exp $
|
||||
|
||||
DISTNAME= fastp-0.20.0
|
||||
# 0.22.0 is the last release that doesn't depend on the non-portable
|
||||
# Intel isa-l library
|
||||
DISTNAME= fastp-0.22.0
|
||||
CATEGORIES= biology
|
||||
MASTER_SITES= ${MASTER_SITE_GITHUB:=OpenGene/}
|
||||
GITHUB_TAG= v${PKGVERSION_NOREV}
|
||||
|
|
@ -15,12 +17,6 @@ USE_TOOLS+= gmake
|
|||
BUILD_TARGET= fastp
|
||||
PTHREAD_AUTO_VARS= yes
|
||||
|
||||
# src/stats.cpp: In member function 'void Stats::statRead(Read*)':
|
||||
# src/stats.cpp:248:29: error: array subscript has type 'char' [-Werror=char-subscripts]
|
||||
# mCycleQ30Bases[b][i]++;
|
||||
# Maybe fix this later.
|
||||
BUILDLINK_TRANSFORM+= rm:-Werror=char-subscripts
|
||||
|
||||
post-install:
|
||||
${STRIP} ${DESTDIR}${PREFIX}/bin/fastp
|
||||
|
||||
|
|
|
|||
|
|
@ -1,2 +1,2 @@
|
|||
@comment $NetBSD: PLIST,v 1.1 2019/05/04 16:15:25 bacon Exp $
|
||||
@comment $NetBSD: PLIST,v 1.2 2023/06/01 13:03:53 bacon Exp $
|
||||
bin/fastp
|
||||
|
|
|
|||
|
|
@ -1,6 +1,7 @@
|
|||
$NetBSD: distinfo,v 1.3 2021/10/26 10:03:38 nia Exp $
|
||||
$NetBSD: distinfo,v 1.4 2023/06/01 13:03:53 bacon Exp $
|
||||
|
||||
BLAKE2s (fastp-0.20.0.tar.gz) = 1096c02c241da76f04cbf485abd3a348b1c87af88e7ba3adb2fe5b0ff811c327
|
||||
SHA512 (fastp-0.20.0.tar.gz) = 33349b761283a42fb9eaf045ab7f839d5ec335fb394e277519b87f8c95cf682027ab183b174a1b82d908a3e4d1d65ac63a88c30efea04d93a08f559c1a7a732c
|
||||
Size (fastp-0.20.0.tar.gz) = 139422 bytes
|
||||
SHA1 (patch-Makefile) = 52fa55ead7d384b8c758e7a2d14680a53f61e623
|
||||
BLAKE2s (fastp-0.22.0.tar.gz) = fbeed45925f33bde6020054e68affd30b076a81a43f383650cf5c8b6e0d09e7d
|
||||
SHA512 (fastp-0.22.0.tar.gz) = 661e61c78fd77347e23380bb0da79e4269ef0acf7350e2b95dd104b85083db55e12b52330bb8fbcaf25554f22d649315db05e083704b8bdabf1e5fb345e34c41
|
||||
Size (fastp-0.22.0.tar.gz) = 141257 bytes
|
||||
SHA1 (patch-Makefile) = d55955d62ede0e5fad1be39c937fedb7e79b746d
|
||||
SHA1 (patch-src_main.cpp) = d28fb587c72b59f4c86bc51fd66874344a9dd43d
|
||||
|
|
|
|||
|
|
@ -1,31 +1,30 @@
|
|||
$NetBSD: patch-Makefile,v 1.1 2019/05/04 16:15:25 bacon Exp $
|
||||
$NetBSD: patch-Makefile,v 1.2 2023/06/01 13:03:53 bacon Exp $
|
||||
|
||||
# Add destdir support, install-strip, and respect LDFLAGS
|
||||
# Respect env
|
||||
|
||||
--- Makefile.orig 2019-04-17 03:23:22.000000000 +0000
|
||||
--- Makefile.orig 2021-08-24 14:00:31.000000000 +0000
|
||||
+++ Makefile
|
||||
@@ -3,9 +3,11 @@ DIR_SRC := ./src
|
||||
DIR_OBJ := ./obj
|
||||
|
||||
PREFIX ?= /usr/local
|
||||
+DESTDIR ?=
|
||||
BINDIR ?= $(PREFIX)/bin
|
||||
@@ -7,6 +7,8 @@ BINDIR ?= $(PREFIX)/bin
|
||||
INCLUDE_DIRS ?=
|
||||
LIBRARY_DIRS ?=
|
||||
+STRIP ?= strip
|
||||
|
||||
+STRIP ?= strip
|
||||
+
|
||||
SRC := $(wildcard ${DIR_SRC}/*.cpp)
|
||||
OBJ := $(patsubst %.cpp,${DIR_OBJ}/%.o,$(notdir ${SRC}))
|
||||
@@ -15,13 +17,14 @@ TARGET := fastp
|
||||
|
||||
@@ -15,13 +17,17 @@ TARGET := fastp
|
||||
BIN_TARGET := ${TARGET}
|
||||
|
||||
CXX ?= g++
|
||||
-CXXFLAGS := -std=c++11 -g -O3 -I${DIR_INC} $(foreach includedir,$(INCLUDE_DIRS),-I$(includedir)) ${CXXFLAGS}
|
||||
-LIBS := -lz -lpthread
|
||||
-LD_FLAGS := $(foreach librarydir,$(LIBRARY_DIRS),-L$(librarydir)) $(LIBS) $(LD_FLAGS)
|
||||
+# Optional flags that the user can override by setting CXXFLAGS in the
|
||||
+# env or make argument
|
||||
+CXXFLAGS ?= -g -O3
|
||||
+# Required flags
|
||||
+CXXFLAGS += -std=c++11 -I${DIR_INC} $(foreach includedir,$(INCLUDE_DIRS),-I$(includedir))
|
||||
+LIBS := -lz
|
||||
LIBS := -lz -lpthread
|
||||
-LD_FLAGS := $(foreach librarydir,$(LIBRARY_DIRS),-L$(librarydir)) $(LIBS) $(LD_FLAGS)
|
||||
+LDFLAGS += $(foreach librarydir,$(LIBRARY_DIRS),-L$(librarydir)) $(LIBS)
|
||||
|
||||
|
||||
|
|
@ -35,14 +34,17 @@ $NetBSD: patch-Makefile,v 1.1 2019/05/04 16:15:25 bacon Exp $
|
|||
|
||||
${DIR_OBJ}/%.o:${DIR_SRC}/%.cpp make_obj_dir
|
||||
$(CXX) -c $< -o $@ $(CXXFLAGS)
|
||||
@@ -38,5 +41,9 @@ make_obj_dir:
|
||||
@@ -43,6 +49,12 @@ make_obj_dir:
|
||||
mkdir $(DIR_OBJ) ; \
|
||||
fi
|
||||
|
||||
+# Respect DESTDIR for staged installs (used by most package managers)
|
||||
install:
|
||||
- install $(TARGET) $(BINDIR)/$(TARGET)
|
||||
+ install -d $(DESTDIR)$(BINDIR)
|
||||
+ mkdir $(DESTDIR)$(BINDIR)
|
||||
+ install $(TARGET) $(DESTDIR)$(BINDIR)/$(TARGET)
|
||||
@echo "Installed."
|
||||
+
|
||||
+# Many package managers use install-strip target if debugging is not enabled
|
||||
+install-strip: install
|
||||
+ $(STRIP) $(DESTDIR)$(BINDIR)/$(TARGET)
|
||||
|
|
|
|||
21
biology/fastp/patches/patch-src_main.cpp
Normal file
21
biology/fastp/patches/patch-src_main.cpp
Normal file
|
|
@ -0,0 +1,21 @@
|
|||
$NetBSD: patch-src_main.cpp,v 1.1 2023/06/01 13:03:53 bacon Exp $
|
||||
|
||||
# Make sure main() returns a value
|
||||
|
||||
--- 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;
|
||||
Loading…
Reference in a new issue