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Date:      Tue, 26 Oct 2004 07:20:23 GMT
From:      "Choe, Cheng-Dae" <whitekid@gmail.com>
To:        freebsd-ports-bugs@FreeBSD.org
Subject:   Re: ports/73149: [New ports]: biology/mpiblast
Message-ID:  <200410260720.i9Q7KNsw007775@freefall.freebsd.org>

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The following reply was made to PR ports/73149; it has been noted by GNATS.

From: "Choe, Cheng-Dae" <whitekid@gmail.com>
To: freebsd-gnats-submit@freebsd.org, freebsd-ports-bugs@freebsd.org
Cc:  
Subject: Re: ports/73149: [New ports]: biology/mpiblast
Date: Tue, 26 Oct 2004 16:17:40 +0900

 Sorry again. I missed patch (files/*) again.
 
 Here is the REALLY correct pr for biology/mpiblast. I so sorry...
 ----------------------------
 # This is a shell archive.  Save it in a file, remove anything before
 # this line, and then unpack it by entering "sh file".  Note, it may
 # create directories; files and directories will be owned by you and
 # have default permissions.
 #
 # This archive contains:
 #
 #       mpiblast
 #       mpiblast/Makefile
 #       mpiblast/distinfo
 #       mpiblast/pkg-descr
 #       mpiblast/pkg-message
 #       mpiblast/pkg-plist
 #       mpiblast/files
 #       mpiblast/files/patch-src_Makefile.in
 #       mpiblast/files/patch-src_Makefile.am
 #
 echo c - mpiblast
 mkdir -p mpiblast > /dev/null 2>&1
 echo x - mpiblast/Makefile
 sed 's/^X//' >mpiblast/Makefile << 'END-of-mpiblast/Makefile'
 X# New ports collection makefile for:    mpiblast
 X# Date created:         23 October 2004
 X# Whom:                 whitekid
 X#
 X# $FreeBSD$
 X#
 X
 XPORTNAME=      mpiblast
 XPORTVERSION=   1.2.1
 XPORTREVISION=  0
 XCATEGORIES=    biology parallel
 XMASTER_SITES=  http://mpiblast.lanl.gov/releases/
 XDISTNAME=      mpiBLAST-${PORTVERSION}
 X
 XMAINTAINER=    whitekid@gmail.com
 XCOMMENT=       A parallelization for NCBI BLAST
 X
 XBUILD_DEPENDS= ${NONEXISTENT}:${PORTSDIR}/biology/ncbi-toolkit:build \
 X       ${LOCALBASE}/include/mpi.h:${PORTSDIR}/net/lam
 X
 XGNU_CONFIGURE= yes
 X
 XCONFIGURE_ARGS=        --with-ncbi=${PORTSDIR}/biology/ncbi-toolkit/work/ncbi
 X
 XDOCS=  AUTHORS COPYING ChangeLog INSTALL LICENSE NEWS README TODO
 XDATAS= WWWBlastWrap.pl
 X
 Xpost-install:
 X       @${INSTALL_DATA} ${WRKSRC}/mpiblast.conf
 ${PREFIX}/etc/mpiblast.conf.sample
 X
 X.if !defined(NOPORTDOCS)
 X       @${MKDIR} ${DOCSDIR}
 X.for file in ${DOCS}
 X       @${INSTALL_DATA} ${WRKSRC}/${file} ${DOCSDIR}
 X.endfor
 X
 X       @${MKDIR} ${DATADIR}
 X.for file in ${DATAS}
 X       @${INSTALL_DATA} ${WRKSRC}/${file} ${DATADIR}
 X.endfor
 X.endif
 X
 X.include <bsd.port.mk>
 END-of-mpiblast/Makefile
 echo x - mpiblast/distinfo
 sed 's/^X//' >mpiblast/distinfo << 'END-of-mpiblast/distinfo'
 XMD5 (mpiBLAST-1.2.1.tar.gz) = 7724f4fbdcecd00d0cc597214efd54e1
 XSIZE (mpiBLAST-1.2.1.tar.gz) = 170513
 END-of-mpiblast/distinfo
 echo x - mpiblast/pkg-descr
 sed 's/^X//' >mpiblast/pkg-descr << 'END-of-mpiblast/pkg-descr'
 XmpiBLAST is a freely available open source parallelization of NCBI BLAST.
 XmpiBLAST segments the BLAST database and distributes it across cluster nodes,
 Xpermitting BLAST queries to be processed on many nodes simultaneously. mpiBLAST
 Xis based on MPI. The current release runs under Linux and Windows, and will
 Xprobably work on other varieties of Unix as well.
 X
 XWWW: http://mpiblast.lanl.gov/
 END-of-mpiblast/pkg-descr
 echo x - mpiblast/pkg-message
 sed 's/^X//' >mpiblast/pkg-message << 'END-of-mpiblast/pkg-message'
 X--------------------------------------------------------------------------
 X
 XThe mpiBLAST package has been successfully installed.
 X
 XNB:  A sample configuration file has been installed to %%PREFIX%%/etc as
 X"mpiblast.conf.sample".  This may be renamed to "mpiblast.conf" and edited
 Xto suit the requirements of a particular site.
 X
 XPlease read %%DOCSDIR%%/README file for detail.
 X
 X--------------------------------------------------------------------------
 END-of-mpiblast/pkg-message
 echo x - mpiblast/pkg-plist
 sed 's/^X//' >mpiblast/pkg-plist << 'END-of-mpiblast/pkg-plist'
 Xbin/mpiblast
 Xbin/mpiformatdb
 Xetc/mpiblast.conf
 Xetc/mpiblast.conf.sample
 X%%PORTDOCS%%%%DOCSDIR%%/AUTHORS
 X%%PORTDOCS%%%%DOCSDIR%%/COPYING
 X%%PORTDOCS%%%%DOCSDIR%%/ChangeLog
 X%%PORTDOCS%%%%DOCSDIR%%/INSTALL
 X%%PORTDOCS%%%%DOCSDIR%%/LICENSE
 X%%PORTDOCS%%%%DOCSDIR%%/NEWS
 X%%PORTDOCS%%%%DOCSDIR%%/README
 X%%PORTDOCS%%%%DOCSDIR%%/TODO
 X%%DATADIR%%/WWWBlastWrap.pl
 X@dirrm %%DATADIR%%
 X@dirrm %%DOCSDIR%%
 END-of-mpiblast/pkg-plist
 echo c - mpiblast/files
 mkdir -p mpiblast/files > /dev/null 2>&1
 echo x - mpiblast/files/patch-src_Makefile.in
 sed 's/^X//' >mpiblast/files/patch-src_Makefile.in <<
 'END-of-mpiblast/files/patch-src_Makefile.in'
 X
 X$FreeBSD$
 X
 X--- src/Makefile.in.orig
 X+++ src/Makefile.in
 X@@ -184,7 +184,7 @@
 X mpiblast_SOURCES = $(mpiblastsrc)
 X EXTRA_mpiblast_SOURCES = getopt.c getopt.h getopt1.c
 X
 X-mpiblast_LDADD = @GETOPT_LONG_SYSTEM@
 @CONFIG_NCBIDIR@/build/ncbithr.o  -lncbitool -lncbiobj -lncbi
 -L@CONFIG_NCBIDIR@/lib/  -lm -lpthread
 X+mpiblast_LDADD = @GETOPT_LONG_SYSTEM@
 @CONFIG_NCBIDIR@/build/ncbithr.o  -lncbitool -lncbiobj -lncbi
 -L@CONFIG_NCBIDIR@/lib/  -lm -lc_r
 X mpiblast_DEPENDENCIES = @GETOPT_LONG_SYSTEM@
 X mpiblast_CPPFLAGS = -DUSING_MPI
 X
 X@@ -194,7 +194,7 @@
 X
 X mpiformatdb_SOURCES = $(mpiformatdbsrc)
 X
 X-mpiformatdb_LDADD = @GETOPT_LONG_SYSTEM@ formatdb.o
 @CONFIG_NCBIDIR@/build/ncbithr.o  -lncbitool -lncbiobj -lncbi
 -L@CONFIG_NCBIDIR@/lib/  -lm -lpthread
 X+mpiformatdb_LDADD = @GETOPT_LONG_SYSTEM@ formatdb.o
 @CONFIG_NCBIDIR@/build/ncbithr.o  -lncbitool -lncbiobj -lncbi
 -L@CONFIG_NCBIDIR@/lib/  -lm -lc_r
 X mpiformatdb_DEPENDENCIES = @GETOPT_LONG_SYSTEM@ formatdb
 X
 X mpiformatdb_INCLUDES = -I$(top_srcdir)/include/ -I@CONFIG_NCBIDIR@/include/
 END-of-mpiblast/files/patch-src_Makefile.in
 echo x - mpiblast/files/patch-src_Makefile.am
 sed 's/^X//' >mpiblast/files/patch-src_Makefile.am <<
 'END-of-mpiblast/files/patch-src_Makefile.am'
 X
 X$FreeBSD$
 X
 X--- src/Makefile.am.orig
 X+++ src/Makefile.am
 X@@ -69,7 +69,7 @@
 X mpiblast_SOURCES = $(mpiblastsrc)
 X EXTRA_mpiblast_SOURCES = getopt.c getopt.h getopt1.c
 X
 X-mpiblast_LDADD = @GETOPT_LONG_SYSTEM@
 @CONFIG_NCBIDIR@/build/ncbithr.o  -lncbitool -lncbiobj -lncbi
 -L@CONFIG_NCBIDIR@/lib/  -lm -lpthread
 X+mpiblast_LDADD = @GETOPT_LONG_SYSTEM@
 @CONFIG_NCBIDIR@/build/ncbithr.o  -lncbitool -lncbiobj -lncbi
 -L@CONFIG_NCBIDIR@/lib/  -lm -lc_r
 X mpiblast_DEPENDENCIES = @GETOPT_LONG_SYSTEM@
 X mpiblast_CPPFLAGS = -DUSING_MPI
 X
 X@@ -78,7 +78,7 @@
 X                               fragment_list.cpp fragment_list.hpp
 db_spec.hpp db_spec.cpp
 X mpiformatdb_SOURCES = $(mpiformatdbsrc)
 X
 X-mpiformatdb_LDADD = @GETOPT_LONG_SYSTEM@ formatdb.o
 @CONFIG_NCBIDIR@/build/ncbithr.o  -lncbitool -lncbiobj -lncbi
 -L@CONFIG_NCBIDIR@/lib/  -lm -lpthread
 X+mpiformatdb_LDADD = @GETOPT_LONG_SYSTEM@ formatdb.o
 @CONFIG_NCBIDIR@/build/ncbithr.o  -lncbitool -lncbiobj -lncbi
 -L@CONFIG_NCBIDIR@/lib/  -lm -lc_r
 X mpiformatdb_DEPENDENCIES = @GETOPT_LONG_SYSTEM@ formatdb
 X
 X mpiformatdb_INCLUDES = -I$(top_srcdir)/include/ -I@CONFIG_NCBIDIR@/include/
 END-of-mpiblast/files/patch-src_Makefile.am
 exit
 ----------------------------



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