ports/73149: [New ports]: biology/mpiblast

Choe, Cheng-Dae whitekid at gmail.com
Tue Oct 26 07:17:41 UTC 2004 

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 at 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 at dirrm %%DATADIR%%
X at 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 at CONFIG_NCBIDIR@/lib/  -lm -lpthread
X+mpiblast_LDADD = @GETOPT_LONG_SYSTEM@
@CONFIG_NCBIDIR@/build/ncbithr.o  -lncbitool -lncbiobj -lncbi
-L at 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 = $(mpiformatdbsrc)
X
X-mpiformatdb_LDADD = @GETOPT_LONG_SYSTEM@ formatdb.o
@CONFIG_NCBIDIR@/build/ncbithr.o  -lncbitool -lncbiobj -lncbi
-L at CONFIG_NCBIDIR@/lib/  -lm -lpthread
X+mpiformatdb_LDADD = @GETOPT_LONG_SYSTEM@ formatdb.o
@CONFIG_NCBIDIR@/build/ncbithr.o  -lncbitool -lncbiobj -lncbi
-L at CONFIG_NCBIDIR@/lib/  -lm -lc_r
X mpiformatdb_DEPENDENCIES = @GETOPT_LONG_SYSTEM@ formatdb
X
X mpiformatdb_INCLUDES = -I$(top_srcdir)/include/ -I at 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 at CONFIG_NCBIDIR@/lib/  -lm -lpthread
X+mpiblast_LDADD = @GETOPT_LONG_SYSTEM@
@CONFIG_NCBIDIR@/build/ncbithr.o  -lncbitool -lncbiobj -lncbi
-L at 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 = $(mpiformatdbsrc)
X
X-mpiformatdb_LDADD = @GETOPT_LONG_SYSTEM@ formatdb.o
@CONFIG_NCBIDIR@/build/ncbithr.o  -lncbitool -lncbiobj -lncbi
-L at CONFIG_NCBIDIR@/lib/  -lm -lpthread
X+mpiformatdb_LDADD = @GETOPT_LONG_SYSTEM@ formatdb.o
@CONFIG_NCBIDIR@/build/ncbithr.o  -lncbitool -lncbiobj -lncbi
-L at CONFIG_NCBIDIR@/lib/  -lm -lc_r
X mpiformatdb_DEPENDENCIES = @GETOPT_LONG_SYSTEM@ formatdb
X
X mpiformatdb_INCLUDES = -I$(top_srcdir)/include/ -I at CONFIG_NCBIDIR@/include/
END-of-mpiblast/files/patch-src_Makefile.am
exit
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