Date: Fri, 3 May 2019 14:41:58 +0000 (UTC) From: "Jason W. Bacon" <jwb@FreeBSD.org> To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r500737 - in head/biology: . fastp fastp/files Message-ID: <201905031441.x43Efw3K080622@repo.freebsd.org>
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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@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
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