diff options
author | bacon <bacon@pkgsrc.org> | 2019-05-04 16:15:25 +0000 |
---|---|---|
committer | bacon <bacon@pkgsrc.org> | 2019-05-04 16:15:25 +0000 |
commit | 67cb5604296f1815f080e307c98bc4b190d324e1 (patch) | |
tree | 81e77b25418640d64283260a69ce4469efb27d46 /biology | |
parent | b357d09f9028c29d3e31761c0ae55c44ac2d358f (diff) | |
download | pkgsrc-67cb5604296f1815f080e307c98bc4b190d324e1.tar.gz |
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.
Diffstat (limited to 'biology')
-rw-r--r-- | biology/fastp/DESCR | 3 | ||||
-rw-r--r-- | biology/fastp/Makefile | 23 | ||||
-rw-r--r-- | biology/fastp/PLIST | 2 | ||||
-rw-r--r-- | biology/fastp/distinfo | 7 | ||||
-rw-r--r-- | biology/fastp/patches/patch-Makefile | 48 |
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) |