biology/fastp: import fastp-0.20.0

fastp is a tool designed to provide fast all-in-one preprocessing for FastQ
files. This tool is developed in C++ with multithreading supported to afford
high performance.

5 files changed, 83 insertions, 0 deletions

diff --git a/biology/fastp/DESCR b/biology/fastp/DESCR
new file mode 100644
index 00000000000..e799d025d69
--- /dev/null
+++ b/biology/fastp/DESCR
@@ -0,0 +1,3 @@
+fastp is a tool designed to provide fast all-in-one preprocessing for FastQ
+files. This tool is developed in C++ with multithreading supported to afford
+high performance.
diff --git a/biology/fastp/Makefile b/biology/fastp/Makefile
new file mode 100644
index 00000000000..99304103002
--- /dev/null
+++ b/biology/fastp/Makefile
@@ -0,0 +1,23 @@
+# $NetBSD: Makefile,v 1.1 2019/05/04 16:15:25 bacon Exp $
+
+DISTNAME=	fastp-0.20.0
+CATEGORIES=	biology
+MASTER_SITES=	${MASTER_SITE_GITHUB:=OpenGene/}
+GITHUB_TAG=	v${PKGVERSION_NOREV}
+
+MAINTAINER=	bacon@NetBSD.org
+HOMEPAGE=	https://github.com/OpenGene/fastp
+COMMENT=	Ultra-fast all-in-one FASTQ preprocessor
+LICENSE=	mit
+
+USE_LANGUAGES=		c c++
+USE_TOOLS+=		gmake
+BUILD_TARGET=		fastp
+PTHREAD_AUTO_VARS=	yes
+
+post-install:
+	${STRIP} ${DESTDIR}${PREFIX}/bin/fastp
+
+.include "../../devel/zlib/buildlink3.mk"
+.include "../../mk/pthread.buildlink3.mk"
+.include "../../mk/bsd.pkg.mk"
diff --git a/biology/fastp/PLIST b/biology/fastp/PLIST
new file mode 100644
index 00000000000..d7dd5eb8404
--- /dev/null
+++ b/biology/fastp/PLIST
@@ -0,0 +1,2 @@
+@comment $NetBSD: PLIST,v 1.1 2019/05/04 16:15:25 bacon Exp $
+bin/fastp
diff --git a/biology/fastp/distinfo b/biology/fastp/distinfo
new file mode 100644
index 00000000000..81baf64c23c
--- /dev/null
+++ b/biology/fastp/distinfo
@@ -0,0 +1,7 @@
+$NetBSD: distinfo,v 1.1 2019/05/04 16:15:25 bacon Exp $
+
+SHA1 (fastp-0.20.0.tar.gz) = 657888d18b40aa18aa6d68e31a5e930ae8cf1606
+RMD160 (fastp-0.20.0.tar.gz) = 0ad6a0eb389e31855f1fa95a089aaa653164f88e
+SHA512 (fastp-0.20.0.tar.gz) = 33349b761283a42fb9eaf045ab7f839d5ec335fb394e277519b87f8c95cf682027ab183b174a1b82d908a3e4d1d65ac63a88c30efea04d93a08f559c1a7a732c
+Size (fastp-0.20.0.tar.gz) = 139422 bytes
+SHA1 (patch-Makefile) = 52fa55ead7d384b8c758e7a2d14680a53f61e623
diff --git a/biology/fastp/patches/patch-Makefile b/biology/fastp/patches/patch-Makefile
new file mode 100644
index 00000000000..d863ed2e9aa
--- /dev/null
+++ b/biology/fastp/patches/patch-Makefile
@@ -0,0 +1,48 @@
+$NetBSD: patch-Makefile,v 1.1 2019/05/04 16:15:25 bacon Exp $
+
+# Add destdir support, install-strip, and respect LDFLAGS
+
+--- Makefile.orig	2019-04-17 03:23:22.000000000 +0000
++++ Makefile
+@@ -3,9 +3,11 @@ DIR_SRC := ./src
+ DIR_OBJ := ./obj
+ 
+ PREFIX ?= /usr/local
++DESTDIR ?=
+ BINDIR ?= $(PREFIX)/bin
+ INCLUDE_DIRS ?=
+ LIBRARY_DIRS ?=
++STRIP ?= strip
+ 
+ SRC := $(wildcard ${DIR_SRC}/*.cpp)
+ OBJ := $(patsubst %.cpp,${DIR_OBJ}/%.o,$(notdir ${SRC}))
+@@ -15,13 +17,14 @@ 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) $(LD_FLAGS)
++CXXFLAGS ?= -g -O3
++CXXFLAGS += -std=c++11 -I${DIR_INC} $(foreach includedir,$(INCLUDE_DIRS),-I$(includedir))
++LIBS := -lz
++LDFLAGS += $(foreach librarydir,$(LIBRARY_DIRS),-L$(librarydir)) $(LIBS)
+ 
+ 
+ ${BIN_TARGET}:${OBJ}
+-	$(CXX) $(OBJ) -o $@ $(LD_FLAGS)
++	$(CXX) $(OBJ) -o $@ $(LDFLAGS)
+ 
+ ${DIR_OBJ}/%.o:${DIR_SRC}/%.cpp make_obj_dir
+ 	$(CXX) -c $< -o $@ $(CXXFLAGS)
+@@ -38,5 +41,9 @@ make_obj_dir:
+ 	fi
+ 
+ install:
+-	install $(TARGET) $(BINDIR)/$(TARGET)
++	install -d $(DESTDIR)$(BINDIR)
++	install $(TARGET) $(DESTDIR)$(BINDIR)/$(TARGET)
+ 	@echo "Installed."
++
++install-strip: install
++	$(STRIP) $(DESTDIR)$(BINDIR)/$(TARGET)