Date: Mon, 16 Apr 2018 14:50:46 +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: r467485 - in head/biology: . fastahack fastahack/files Message-ID: <201804161450.w3GEokTq050411@repo.freebsd.org>
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Author: jwb Date: Mon Apr 16 14:50:46 2018 New Revision: 467485 URL: https://svnweb.freebsd.org/changeset/ports/467485 Log: biology/fastahack: Utility for indexing and sequence extraction from FASTA files Approved by: jrm (mentor) Differential Revision: https://reviews.freebsd.org/D15080 Added: head/biology/fastahack/ head/biology/fastahack/Makefile (contents, props changed) head/biology/fastahack/distinfo (contents, props changed) head/biology/fastahack/files/ head/biology/fastahack/files/Makefile (contents, props changed) head/biology/fastahack/pkg-descr (contents, props changed) head/biology/fastahack/pkg-plist (contents, props changed) Modified: head/biology/Makefile Modified: head/biology/Makefile ============================================================================== --- head/biology/Makefile Mon Apr 16 13:30:58 2018 (r467484) +++ head/biology/Makefile Mon Apr 16 14:50:46 2018 (r467485) @@ -26,6 +26,7 @@ SUBDIR += emboss SUBDIR += fasta SUBDIR += fasta3 + SUBDIR += fastahack SUBDIR += fastdnaml SUBDIR += fastool SUBDIR += fastqc Added: head/biology/fastahack/Makefile ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/fastahack/Makefile Mon Apr 16 14:50:46 2018 (r467485) @@ -0,0 +1,19 @@ +# $FreeBSD$ + +PORTNAME= fastahack +DISTVERSION= g20160702 +CATEGORIES= biology + +MAINTAINER= jwb@FreeBSD.org +COMMENT= Utility for indexing and sequence extraction from FASTA files + +LICENSE= GPLv2 + +USE_GITHUB= yes +GH_ACCOUNT= ekg +GH_TAGNAME= bbc645f2f7966cb7b44446200c02627c3168b399 + +MAKEFILE= ${FILESDIR}/Makefile +INSTALL_TARGET= install-strip + +.include <bsd.port.mk> Added: head/biology/fastahack/distinfo ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/fastahack/distinfo Mon Apr 16 14:50:46 2018 (r467485) @@ -0,0 +1,3 @@ +TIMESTAMP = 1523600462 +SHA256 (ekg-fastahack-g20160702-bbc645f2f7966cb7b44446200c02627c3168b399_GH0.tar.gz) = dc8ef61765b7720fd2d163143696f1c82251bfd906ac5261642e7230d81d5da6 +SIZE (ekg-fastahack-g20160702-bbc645f2f7966cb7b44446200c02627c3168b399_GH0.tar.gz) = 18200 Added: head/biology/fastahack/files/Makefile ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/fastahack/files/Makefile Mon Apr 16 14:50:46 2018 (r467485) @@ -0,0 +1,62 @@ + +# Use ?= to allow overriding from the env or command-line, e.g. +# +# make CXXFLAGS="-O3 -fPIC" install +# +# Package managers will override many of these variables automatically, so +# this is aimed at making it easy to create packages (Debian packages, +# FreeBSD ports, MacPorts, pkgsrc, etc.) + +CXX ?= c++ +CXXFLAGS ?= -O3 +DESTDIR ?= stage +PREFIX ?= /usr/local +STRIP ?= strip +INSTALL ?= install -c +MKDIR ?= mkdir -p +AR ?= ar + +# Required flags that we shouldn't override +# Must be compiler-independent +CXXFLAGS += -D_FILE_OFFSET_BITS=64 + +BIN = fastahack +LIB = libfastahack.a +OBJS = Fasta.o split.o disorder.o +MAIN = FastaHack.o + +all: $(BIN) $(LIB) + +$(BIN): $(OBJS) $(MAIN) + $(CXX) $(CXXFLAGS) $(OBJS) $(MAIN) -o $(BIN) + +$(LIB): $(OBJS) + ${AR} -rs $(LIB) $(OBJS) + +FastaHack.o: Fasta.h FastaHack.cpp + $(CXX) $(CXXFLAGS) -c FastaHack.cpp + +Fasta.o: Fasta.h Fasta.cpp + $(CXX) $(CXXFLAGS) -c Fasta.cpp + +split.o: split.h split.cpp + $(CXX) $(CXXFLAGS) -c split.cpp + +disorder.o: disorder.c disorder.h + $(CXX) $(CXXFLAGS) -c disorder.c + +install: all + $(MKDIR) $(DESTDIR)$(PREFIX)/bin + $(MKDIR) $(DESTDIR)$(PREFIX)/include/fastahack + $(MKDIR) $(DESTDIR)$(PREFIX)/lib + $(INSTALL) $(BIN) $(DESTDIR)$(PREFIX)/bin + $(INSTALL) *.h $(DESTDIR)$(PREFIX)/include/fastahack + $(INSTALL) $(LIB) $(DESTDIR)$(PREFIX)/lib + +install-strip: install + $(STRIP) $(DESTDIR)$(PREFIX)/bin/$(BIN) + +clean: + rm -rf $(BIN) $(LIB) $(OBJS) $(DESTDIR) + +.PHONY: clean Added: head/biology/fastahack/pkg-descr ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/fastahack/pkg-descr Mon Apr 16 14:50:46 2018 (r467485) @@ -0,0 +1,7 @@ +Fastahack is a small application for indexing and extracting sequences and +subsequences from FASTA files. The included Fasta.cpp library provides a FASTA +reader and indexer that can be embedded into applications which would benefit +from directly reading subsequences from FASTA files. The library automatically +handles index file generation and use. + +WWW: https://github.com/ekg/fastahack Added: head/biology/fastahack/pkg-plist ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/fastahack/pkg-plist Mon Apr 16 14:50:46 2018 (r467485) @@ -0,0 +1,7 @@ +bin/fastahack +include/fastahack/Fasta.h +include/fastahack/LargeFileSupport.h +include/fastahack/Region.h +include/fastahack/disorder.h +include/fastahack/split.h +lib/libfastahack.a
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