Date: Sat, 14 Apr 2018 23:52:17 +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: r467343 - in head/biology: . tabixpp tabixpp/files Message-ID: <201804142352.w3ENqHRs077564@repo.freebsd.org>
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Author: jwb Date: Sat Apr 14 23:52:16 2018 New Revision: 467343 URL: https://svnweb.freebsd.org/changeset/ports/467343 Log: biology/tabixpp: C++ wrapper to tabix indexer Reviewed by: mat Approved by: jrm (mentor) Differential Revision: https://reviews.freebsd.org/D14977 Added: head/biology/tabixpp/ head/biology/tabixpp/Makefile (contents, props changed) head/biology/tabixpp/distinfo (contents, props changed) head/biology/tabixpp/files/ head/biology/tabixpp/files/Makefile (contents, props changed) head/biology/tabixpp/pkg-descr (contents, props changed) Modified: head/biology/Makefile Modified: head/biology/Makefile ============================================================================== --- head/biology/Makefile Sat Apr 14 22:17:53 2018 (r467342) +++ head/biology/Makefile Sat Apr 14 23:52:16 2018 (r467343) @@ -115,6 +115,7 @@ SUBDIR += stacks SUBDIR += tRNAscan-SE SUBDIR += t_coffee + SUBDIR += tabixpp SUBDIR += tinker SUBDIR += treepuzzle SUBDIR += trimadap Added: head/biology/tabixpp/Makefile ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/tabixpp/Makefile Sat Apr 14 23:52:16 2018 (r467343) @@ -0,0 +1,36 @@ +# $FreeBSD$ + +PORTNAME= tabixpp +DISTVERSIONPREFIX= v +DISTVERSION= 1.0.0-10 +DISTVERSIONSUFFIX= -g6bbe690 +CATEGORIES= biology + +MAINTAINER= jwb@FreeBSD.org +COMMENT= C++ wrapper to tabix indexer + +LICENSE= MIT +LICENSE_FILE= ${WRKSRC}/LICENSE + +LIB_DEPENDS= libhts.so:biology/htslib + +USES= localbase:ldflags +USE_LDCONFIG= yes +USE_GITHUB= yes +GH_ACCOUNT= ekg + +# Disable bundled htslib +MAKE_ENV= HTS_HEADERS='' HTS_LIB='' +MAKEFILE= ${FILESDIR}/Makefile +INSTALL_TARGET= install-strip +PLIST_FILES= bin/tabix++ \ + include/tabix.hpp \ + lib/libtabix.a \ + lib/libtabix.so \ + lib/libtabix.so.1 + +post-install: + ${RLN} ${STAGEDIR}${PREFIX}/lib/libtabix.so.1 \ + ${STAGEDIR}${PREFIX}/lib/libtabix.so + +.include <bsd.port.mk> Added: head/biology/tabixpp/distinfo ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/tabixpp/distinfo Sat Apr 14 23:52:16 2018 (r467343) @@ -0,0 +1,3 @@ +TIMESTAMP = 1522943679 +SHA256 (ekg-tabixpp-v1.0.0-10-g6bbe690_GH0.tar.gz) = 3a83517f77da15bfd48e6fbaa860560e0f1927254c9f1c332759fe086f65154a +SIZE (ekg-tabixpp-v1.0.0-10-g6bbe690_GH0.tar.gz) = 3694 Added: head/biology/tabixpp/files/Makefile ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/tabixpp/files/Makefile Sat Apr 14 23:52:16 2018 (r467343) @@ -0,0 +1,86 @@ + +# 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.) + +CC ?= cc +CXX ?= c++ +CXXFLAGS ?= -g -Wall -O2 #-m64 #-arch ppc +CXXFLAGS += -fPIC +INCLUDES ?= -Ihtslib +HTS_HEADERS ?= htslib/htslib/bgzf.h htslib/htslib/tbx.h +HTS_LIB ?= htslib/libhts.a +LDFLAGS ?= -Lhtslib +LDFLAGS += -L. + +DESTDIR ?= stage +PREFIX ?= /usr/local +STRIP ?= strip +INSTALL ?= install -c +MKDIR ?= mkdir -p +AR ?= ar + +DFLAGS = -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE +BIN = tabix++ +LIB = libtabix.a +SOVERSION = 1 +SLIB = libtabix.so.$(SOVERSION) +OBJS = tabix.o +SUBDIRS = . + +.SUFFIXES:.c .o + +.c.o: + $(CC) -c $(CXXFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@ + +all-recur lib-recur clean-recur cleanlocal-recur install-recur: + @target=`echo $@ | sed s/-recur//`; \ + wdir=`pwd`; \ + list='$(SUBDIRS)'; for subdir in $$list; do \ + cd $$subdir; \ + $(MAKE) CC="$(CC)" DFLAGS="$(DFLAGS)" CXXFLAGS="$(CXXFLAGS)" \ + INCLUDES="$(INCLUDES)" LDFLAGS="$(LDFLAGS)" $$target \ + || exit 1; \ + cd $$wdir; \ + done; + +all: $(BIN) $(LIB) $(SLIB) + +tabix.o: $(HTS_HEADERS) tabix.cpp tabix.hpp + $(CXX) $(CXXFLAGS) -c tabix.cpp $(INCLUDES) + +htslib/libhts.a: + cd htslib && $(MAKE) lib-static + +$(LIB): $(OBJS) + $(AR) rs $(LIB) $(OBJS) + +$(SLIB): $(OBJS) + $(CXX) -shared -Wl,-soname,$(SLIB) -o $(SLIB) $(OBJS) + +tabix++: $(OBJS) main.cpp $(HTS_LIB) + $(CXX) $(CXXFLAGS) -o $@ main.cpp $(OBJS) $(INCLUDES) $(LDFLAGS) \ + -lhts -lpthread -lm -lz + +install: all + $(MKDIR) $(DESTDIR)$(PREFIX)/bin + $(MKDIR) $(DESTDIR)$(PREFIX)/include + $(MKDIR) $(DESTDIR)$(PREFIX)/lib + $(INSTALL) $(BIN) $(DESTDIR)$(PREFIX)/bin + $(INSTALL) *.hpp $(DESTDIR)$(PREFIX)/include + $(INSTALL) $(LIB) $(SLIB) $(DESTDIR)$(PREFIX)/lib + +install-strip: install + $(STRIP) $(DESTDIR)$(PREFIX)/bin/$(BIN) $(DESTDIR)$(PREFIX)/lib/$(SLIB) + +cleanlocal: + rm -rf $(BIN) $(LIB) $(SLIB) $(OBJS) $(DESTDIR) + rm -fr gmon.out *.o a.out *.dSYM $(BIN) *~ *.a tabix.aux tabix.log \ + tabix.pdf *.class libtabix.*.dylib + cd htslib && $(MAKE) clean + +clean: cleanlocal-recur Added: head/biology/tabixpp/pkg-descr ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/tabixpp/pkg-descr Sat Apr 14 23:52:16 2018 (r467343) @@ -0,0 +1,5 @@ +This is a C++ wrapper around tabix project which abstracts some of the details +of opening and jumping in tabix-indexed files. Tabix is a generic indexer for +TAB-delimited genome position files. + +WWW: https://github.com/ekg/tabixpp
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