Date: Fri, 25 Sep 2015 18:37:25 +0000 (UTC) From: Ruslan Makhmatkhanov <rm@FreeBSD.org> To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r397850 - in head/biology: . cdbfasta cdbfasta/files Message-ID: <201509251837.t8PIbPe4080731@repo.freebsd.org>
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Author: rm Date: Fri Sep 25 18:37:24 2015 New Revision: 397850 URL: https://svnweb.freebsd.org/changeset/ports/397850 Log: Fast indexing and retrieval of FASTA records from flat file data bases. WWW: http://sourceforge.net/projects/cdbfasta/ PR: 203233 Submitted by: Jason Bacon <jwbacon@tds.net> Added: head/biology/cdbfasta/ head/biology/cdbfasta/Makefile (contents, props changed) head/biology/cdbfasta/distinfo (contents, props changed) head/biology/cdbfasta/files/ head/biology/cdbfasta/files/patch-Makefile (contents, props changed) head/biology/cdbfasta/pkg-descr (contents, props changed) Modified: head/biology/Makefile Modified: head/biology/Makefile ============================================================================== --- head/biology/Makefile Fri Sep 25 18:35:14 2015 (r397849) +++ head/biology/Makefile Fri Sep 25 18:37:24 2015 (r397850) @@ -12,6 +12,7 @@ SUBDIR += biojava SUBDIR += blat SUBDIR += cd-hit + SUBDIR += cdbfasta SUBDIR += chemeq SUBDIR += clustalw SUBDIR += consed Added: head/biology/cdbfasta/Makefile ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/cdbfasta/Makefile Fri Sep 25 18:37:24 2015 (r397850) @@ -0,0 +1,25 @@ +# Created by: Dan Siercks <dsiercks@uwm.edu> +# $FreeBSD$ + +PORTNAME= cdbfasta +PORTVERSION= 2010.07.22 +CATEGORIES= biology +MASTER_SITES= http://acadix.biz/Ports/distfiles/ \ + http://personalpages.tds.net/~jwbacon/Ports/distfiles/ + +MAINTAINER= jwbacon@tds.net +COMMENT= Fast indexing and retrieval of FASTA records from flat file databases + +# LICENSE= unspecified + +WRKSRC= ${WRKDIR}/${PORTNAME} + +USES= gmake + +PLIST_FILES= bin/cdbfasta bin/cdbyank + +do-install: + ${INSTALL_PROGRAM} ${WRKSRC}/cdbfasta ${STAGEDIR}${PREFIX}/bin + ${INSTALL_PROGRAM} ${WRKSRC}/cdbyank ${STAGEDIR}${PREFIX}/bin + +.include <bsd.port.mk> Added: head/biology/cdbfasta/distinfo ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/cdbfasta/distinfo Fri Sep 25 18:37:24 2015 (r397850) @@ -0,0 +1,2 @@ +SHA256 (cdbfasta-2010.07.22.tar.gz) = 68767e8b2fb9de5a6d68ee16df73293f65e02f05cf2f747a9dd6b8854766722c +SIZE (cdbfasta-2010.07.22.tar.gz) = 59735 Added: head/biology/cdbfasta/files/patch-Makefile ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/cdbfasta/files/patch-Makefile Fri Sep 25 18:37:24 2015 (r397850) @@ -0,0 +1,54 @@ +--- Makefile.orig 2009-12-03 20:17:51 UTC ++++ Makefile +@@ -18,7 +18,10 @@ else + MARCH = + endif + +-CC := g++ ++# Use the correct compiler (CXX, not CC) and respect the environment ++# by using ?= ++CXX ?= g++ ++ + BASEFLAGS = -Wall ${SEARCHDIRS} $(MARCH) -DENABLE_COMPRESSION=0 -D_FILE_OFFSET_BITS=64 \ + -D_LARGEFILE_SOURCE -fno-exceptions -fno-rtti -fno-strict-aliasing \ + -D_REENTRANT +@@ -33,30 +36,30 @@ else + endif + + ifeq ($(findstring nommap,$(MAKECMDGOALS)),) +- CFLAGS = $(DBGFLAGS) $(BASEFLAGS) ++ CXXFLAGS = $(DBGFLAGS) $(BASEFLAGS) + else +- CFLAGS = $(DBGFLAGS) $(BASEFLAGS) -DNO_MMAP ++ CXXFLAGS = $(DBGFLAGS) $(BASEFLAGS) -DNO_MMAP + endif + + %.o : %.c +- ${CC} ${CFLAGS} -c $< -o $@ ++ ${CXX} ${CXXFLAGS} -c $< -o $@ + + %.o : %.cc +- ${CC} ${CFLAGS} -c $< -o $@ ++ ${CXX} ${CXXFLAGS} -c $< -o $@ + + %.o : %.C +- ${CC} ${CFLAGS} -c $< -o $@ ++ ${CXX} ${CXXFLAGS} -c $< -o $@ + + %.o : %.cpp +- ${CC} ${CFLAGS} -c $< -o $@ ++ ${CXX} ${CXXFLAGS} -c $< -o $@ + + %.o : %.cxx +- ${CC} ${CFLAGS} -c $< -o $@ ++ ${CXX} ${CXXFLAGS} -c $< -o $@ + + # C/C++ linker + +-LINKER := g++ +-LDFLAGS = -lz ++LINKER := ${CXX} ++LDFLAGS = -lz + #if ENABLE_COMPRESSION is not needed, + # LDFLAGS = + Added: head/biology/cdbfasta/pkg-descr ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/cdbfasta/pkg-descr Fri Sep 25 18:37:24 2015 (r397850) @@ -0,0 +1,3 @@ +Fast indexing and retrieval of FASTA records from flat file data bases. + +WWW: http://sourceforge.net/projects/cdbfasta/
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