fastp: Ultra-fast all-in-one FASTQ preprocessor

[Jason Bacon <bacon%NetBSD.org@localhost>]

Module Name:	pkgsrc-wip
Committed By:	Jason Bacon <bacon%NetBSD.org@localhost>
Pushed By:	outpaddling
Date:		Fri May 3 10:11:11 2019 -0500
Changeset:	dc53fbf8333e42f6a125103fcd230940d9768466

Modified Files:
	Makefile
Added Files:
	fastp/DESCR
	fastp/Makefile
	fastp/PLIST
	fastp/distinfo
	fastp/patches/patch-Makefile

Log Message:
fastp: Ultra-fast all-in-one FASTQ preprocessor

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=dc53fbf8333e42f6a125103fcd230940d9768466

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

diffstat:
 Makefile                     |  1 +
 fastp/DESCR                  |  3 +++
 fastp/Makefile               | 20 +++++++++++++++++++
 fastp/PLIST                  |  2 ++
 fastp/distinfo               |  7 +++++++
 fastp/patches/patch-Makefile | 47 ++++++++++++++++++++++++++++++++++++++++++++
 6 files changed, 80 insertions(+)

diffs:
diff --git a/Makefile b/Makefile
index e3af4fce07..2fa9d7208a 100644
--- a/Makefile
+++ b/Makefile
@@ -775,6 +775,7 @@ SUBDIR+=	fastaunique
 SUBDIR+=	fastbit
 SUBDIR+=	fastjet
 SUBDIR+=	fastool
+SUBDIR+=	fastp
 SUBDIR+=	fastqc
 SUBDIR+=	fastrpc
 SUBDIR+=	fasttree
diff --git a/fastp/DESCR b/fastp/DESCR
new file mode 100644
index 0000000000..e799d025d6
--- /dev/null
+++ b/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/fastp/Makefile b/fastp/Makefile
new file mode 100644
index 0000000000..22a4fe75c7
--- /dev/null
+++ b/fastp/Makefile
@@ -0,0 +1,20 @@
+# $NetBSD$
+
+DISTNAME=	fastp-0.20.0
+CATEGORIES=	biology
+MASTER_SITES=	${MASTER_SITE_GITHUB:=OpenGene/}
+GITHUB_PROJECT=	fastp
+GITHUB_TAG=	v0.20.0
+
+MAINTAINER=	bacon%NetBSD.org@localhost
+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
+INSTALL_TARGET=	install-strip
+
+.include "../../devel/zlib/buildlink3.mk"
+.include "../../mk/bsd.pkg.mk"
diff --git a/fastp/PLIST b/fastp/PLIST
new file mode 100644
index 0000000000..a4866ebed9
--- /dev/null
+++ b/fastp/PLIST
@@ -0,0 +1,2 @@
+@comment $NetBSD$
+bin/fastp
diff --git a/fastp/distinfo b/fastp/distinfo
new file mode 100644
index 0000000000..44b30514a1
--- /dev/null
+++ b/fastp/distinfo
@@ -0,0 +1,7 @@
+$NetBSD$
+
+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) = 0b3b734474e9fcca8046ed0532834950317e4c6e
diff --git a/fastp/patches/patch-Makefile b/fastp/patches/patch-Makefile
new file mode 100644
index 0000000000..9dc826a171
--- /dev/null
+++ b/fastp/patches/patch-Makefile
@@ -0,0 +1,47 @@
+$NetBSD$
+
+# 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_CMD ?= 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)) ${CXXFLAGS}
++CXXFLAGS ?= -g -O3
++CXXFLAGS += -std=c++11 -I${DIR_INC} $(foreach includedir,$(INCLUDE_DIRS),-I$(includedir))
+ LIBS := -lz -lpthread
+-LD_FLAGS := $(foreach librarydir,$(LIBRARY_DIRS),-L$(librarydir)) $(LIBS) $(LD_FLAGS)
++LDFLAGS := $(foreach librarydir,$(LIBRARY_DIRS),-L$(librarydir)) $(LIBS) $(LDFLAGS)
+ 
+ 
+ ${BIN_TARGET}:${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_CMD) $(DESTDIR)$(BINDIR)/$(TARGET)