Date: Mon, 24 Sep 2001 19:25:16 +1000 (EST) From: Tony Maher <tonym@biolateral.com.au> To: FreeBSD-gnats-submit@freebsd.org Subject: ports/30783: New port: biology/nclever Message-ID: <200109240925.f8O9PGo12291@dt.home>
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>Number: 30783 >Category: ports >Synopsis: New port: biology/nclever >Confidential: no >Severity: non-critical >Priority: low >Responsible: freebsd-ports >State: open >Quarter: >Keywords: >Date-Required: >Class: change-request >Submitter-Id: current-users >Arrival-Date: Mon Sep 24 02:30:01 PDT 2001 >Closed-Date: >Last-Modified: >Originator: Tony Maher >Release: FreeBSD 4.4-STABLE i386 >Organization: BioLateral >Environment: System: FreeBSD dt.home 4.4-STABLE FreeBSD 4.4-STABLE #16: Sun Sep 23 10:11:40 EST 2001 root@dt.home:/usr/obj/usr/src/sys/DT i386 >Description: New port - biology/nclever "NClever is a character-based version of NCBI's Entrez program. It is an interactive tool that allows easy browsing of the Entrez database. More information available at: WWW: ftp://megasun.bch.umontreal.ca/pub/nclever" This software is under GPL licence (COPYING file in the tarball) >How-To-Repeat: >Fix: # 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: # # nclever # nclever/files # nclever/files/patch-main # nclever/files/patch-makefile # nclever/pkg-descr # nclever/distinfo # nclever/Makefile # nclever/pkg-comment # nclever/pkg-plist # echo c - nclever mkdir -p nclever > /dev/null 2>&1 echo c - nclever/files mkdir -p nclever/files > /dev/null 2>&1 echo x - nclever/files/patch-main sed 's/^X//' >nclever/files/patch-main << 'END-of-nclever/files/patch-main' X--- main.c.orig Mon Sep 24 16:34:16 2001 X+++ main.c Mon Sep 24 16:37:26 2001 X@@ -358,7 +358,7 @@ X /* Read a line from stdin */ X static Boolean GetCommand(void) X { X- if (!gets(Command)) return(FALSE); X+ if (!fgets(Command,MAXLINELEN-1,stdin)) return(FALSE); X if (EchoCommands) fprintf(CmdStream,"%s\n",Command); X return(TRUE); X } END-of-nclever/files/patch-main echo x - nclever/files/patch-makefile sed 's/^X//' >nclever/files/patch-makefile << 'END-of-nclever/files/patch-makefile' X--- Makefile.orig Thu Dec 7 11:11:31 2000 X+++ Makefile Thu Dec 7 11:34:11 2000 X@@ -29,7 +29,8 @@ X # NCBI librairies are needed. X X # Set the correct path to the NCBI package X-NCBI = /usr/local/lib/NCBI X+NCBILIB = /usr/local/lib/ncbi X+NCBIINC = /usr/local/include/ncbi X X # Set the name of your ANSI C compiler X CC = gcc X@@ -39,7 +40,7 @@ X LIBSNCBI = -lncbiNacc -lnetentr -lncbicdr -lncbiobj -lnetcli -lncbi X # System linking libraries (these are used under Solaris 2.6; X # adjust according to your site). X-LIBSSYS = -lm -lsocket -lnsl -lxnet X+LIBSSYS = -lm X X # X # Nothing to adjust below this line ! X@@ -50,20 +51,20 @@ X all: nclever X X nclever: $(OBJS) X- $(CC) $(CCFLAGS) -o nclever -L$(NCBI)/lib $(OBJS) $(LIBSNCBI) $(LIBSSYS) X+ $(CC) $(CCFLAGS) -o nclever -L$(NCBILIB) $(OBJS) $(LIBSNCBI) $(LIBSSYS) X strip nclever X X main.o: main.c main.h X- $(CC) $(CCFLAGS) -c -I$(NCBI)/include main.c X+ $(CC) $(CCFLAGS) -c -I$(NCBIINC) main.c X X lists.o: lists.c main.h X- $(CC) $(CCFLAGS) -c -I$(NCBI)/include lists.c X+ $(CC) $(CCFLAGS) -c -I$(NCBIINC) lists.c X X print.o: print.c main.h X- $(CC) $(CCFLAGS) -c -I$(NCBI)/include print.c X+ $(CC) $(CCFLAGS) -c -I$(NCBIINC) print.c X X entinfo.o: entinfo.c main.h X- $(CC) $(CCFLAGS) -c -I$(NCBI)/include entinfo.c X+ $(CC) $(CCFLAGS) -c -I$(NCBIINC) entinfo.c X X clean: X rm *.o END-of-nclever/files/patch-makefile echo x - nclever/pkg-descr sed 's/^X//' >nclever/pkg-descr << 'END-of-nclever/pkg-descr' XNClever is a character-based version of NCBI's Entrez program. It is an Xinteractive tool that allows easy browsing of the Entrez database. X XMore information available at: XWWW: ftp://megasun.bch.umontreal.ca/pub/nclever X X-- XTony Maher <tonym@biolateral.com.au> END-of-nclever/pkg-descr echo x - nclever/distinfo sed 's/^X//' >nclever/distinfo << 'END-of-nclever/distinfo' XMD5 (nclever4.0.tar.Z) = ef1c97fe8769b41e0fa8773848d70836 END-of-nclever/distinfo echo x - nclever/Makefile sed 's/^X//' >nclever/Makefile << 'END-of-nclever/Makefile' X# New ports collection makefile for: nclever X# Date created: 17 August 2001 X# Whom: Tony Maher X# X# $FreeBSD$ X# X XPORTNAME= nclever XPORTVERSION= 4.0 XCATEGORIES= biology XMASTER_SITES= ftp://megasun.bch.umontreal.ca/pub/nclever/ XDISTNAME= nclever4.0 XEXTRACT_SUFX= .tar.Z X XMAINTAINER= tonym@biolateral.com.au X XBUILD_DEPENDS= ${LOCALBASE}/lib/ncbi/libncbi.a:${PORTSDIR}/biology/ncbi-toolkit X XDOCDIR= ${PREFIX}/share/doc/${PORTNAME} X Xdo-install: X @${INSTALL_PROGRAM} ${WRKSRC}/nclever ${PREFIX}/bin X.if !defined(NOPORTSDOCS) X @${MKDIR} ${DOCDIR} X @${INSTALL_DATA} ${WRKSRC}/nclever_manual.txt ${DOCDIR} X @${INSTALL_DATA} ${WRKSRC}/nclever.citation ${DOCDIR} X @${INSTALL_DATA} ${WRKSRC}/sample_script1.txt ${DOCDIR} X @${INSTALL_DATA} ${WRKSRC}/sample_script2.txt ${DOCDIR} X.endif X X.include <bsd.port.mk> END-of-nclever/Makefile echo x - nclever/pkg-comment sed 's/^X//' >nclever/pkg-comment << 'END-of-nclever/pkg-comment' XNClever is a character-based version of NCBI's Entrez program END-of-nclever/pkg-comment echo x - nclever/pkg-plist sed 's/^X//' >nclever/pkg-plist << 'END-of-nclever/pkg-plist' Xbin/nclever Xshare/doc/nclever/nclever.citation Xshare/doc/nclever/nclever_manual.txt Xshare/doc/nclever/sample_script1.txt Xshare/doc/nclever/sample_script2.txt X@dirrm share/doc/nclever END-of-nclever/pkg-plist exit >Release-Note: >Audit-Trail: >Unformatted: To Unsubscribe: send mail to majordomo@FreeBSD.org with "unsubscribe freebsd-ports" in the body of the message
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