svn commit: r500737 - in head/biology: . fastp fastp/files

[Jason W. Bacon]

Author: jwb
Date: Fri May  3 14:41:57 2019
New Revision: 500737
URL: https://svnweb.freebsd.org/changeset/ports/500737

Log:
  biology/fastp: Ultra-fast all-in-one FASTQ preprocessor
  
  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.

Added:
  head/biology/fastp/
  head/biology/fastp/Makefile   (contents, props changed)
  head/biology/fastp/distinfo   (contents, props changed)
  head/biology/fastp/files/
  head/biology/fastp/files/patch-Makefile   (contents, props changed)
  head/biology/fastp/pkg-descr   (contents, props changed)
Modified:
  head/biology/Makefile

Modified: head/biology/Makefile
==============================================================================
--- head/biology/Makefile	Fri May  3 14:31:18 2019	(r500736)
+++ head/biology/Makefile	Fri May  3 14:41:57 2019	(r500737)
@@ -33,6 +33,7 @@
     SUBDIR += fastahack
     SUBDIR += fastdnaml
     SUBDIR += fastool
+    SUBDIR += fastp
     SUBDIR += fastqc
     SUBDIR += fasttree
     SUBDIR += fastx-toolkit

Added: head/biology/fastp/Makefile
==============================================================================
--- /dev/null	00:00:00 1970	(empty, because file is newly added)
+++ head/biology/fastp/Makefile	Fri May  3 14:41:57 2019	(r500737)
@@ -0,0 +1,30 @@
+# $FreeBSD$
+
+PORTNAME=		fastp
+DISTVERSIONPREFIX=	v
+DISTVERSION=		0.20.0
+CATEGORIES=		biology
+
+MAINTAINER=	jwb at FreeBSD.org
+COMMENT=	Ultra-fast all-in-one FASTQ preprocessor
+
+LICENSE=	MIT
+LICENSE_FILE=	${WRKSRC}/LICENSE
+
+USES=		compiler:c++11-lang gmake
+USE_GITHUB=	yes
+
+GH_ACCOUNT=	OpenGene
+
+ALL_TARGET=	fastp
+INSTALL_TARGET=	install-strip
+PLIST_FILES=	bin/fastp
+
+.include <bsd.port.pre.mk>
+
+# Force newer compiler on platforms using GCC 4.2 as base
+.if ${CHOSEN_COMPILER_TYPE} == gcc
+USE_GCC=	yes
+.endif
+
+.include <bsd.port.post.mk>

Added: head/biology/fastp/distinfo
==============================================================================
--- /dev/null	00:00:00 1970	(empty, because file is newly added)
+++ head/biology/fastp/distinfo	Fri May  3 14:41:57 2019	(r500737)
@@ -0,0 +1,3 @@
+TIMESTAMP = 1556889058
+SHA256 (OpenGene-fastp-v0.20.0_GH0.tar.gz) = 8d751d2746db11ff233032fc49e3bcc8b53758dd4596fdcf4b4099a4d702ac22
+SIZE (OpenGene-fastp-v0.20.0_GH0.tar.gz) = 139422

Added: head/biology/fastp/files/patch-Makefile
==============================================================================
--- /dev/null	00:00:00 1970	(empty, because file is newly added)
+++ head/biology/fastp/files/patch-Makefile	Fri May  3 14:41:57 2019	(r500737)
@@ -0,0 +1,34 @@
+--- Makefile.orig	2019-04-17 03:23:22 UTC
++++ 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}))
+@@ -15,7 +17,8 @@ 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)
+ 
+@@ -38,5 +41,8 @@ make_obj_dir:
+ 	fi
+ 
+ install:
+-	install $(TARGET) $(BINDIR)/$(TARGET)
++	install $(TARGET) $(DESTDIR)$(BINDIR)/$(TARGET)
+ 	@echo "Installed."
++
++install-strip: install
++	$(STRIP_CMD) $(DESTDIR)$(BINDIR)/$(TARGET)

Added: head/biology/fastp/pkg-descr
==============================================================================
--- /dev/null	00:00:00 1970	(empty, because file is newly added)
+++ head/biology/fastp/pkg-descr	Fri May  3 14:41:57 2019	(r500737)
@@ -0,0 +1,5 @@
+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.
+
+WWW: https://github.com/OpenGene/fastp