Add nclever 4.0, a character-based version of NCBI's Entrez program.

PR:		30783
Submitted by:	Tony Maher <tonym@biolateral.com.au>

7 files changed, 104 insertions, 0 deletions

diff --git a/biology/nclever/Makefile b/biology/nclever/Makefile
new file mode 100644
index 000000000000..e512c5e14bda
--- /dev/null
+++ b/biology/nclever/Makefile
@@ -0,0 +1,30 @@
+# New ports collection makefile for:	nclever
+# Date created:				17 August 2001
+# Whom:			 		Tony Maher
+#
+# $FreeBSD$
+#
+
+PORTNAME=	nclever
+PORTVERSION=	4.0
+CATEGORIES=	biology
+MASTER_SITES=	ftp://megasun.bch.umontreal.ca/pub/nclever/
+DISTNAME=	${PORTNAME}${PORTVERSION}
+EXTRACT_SUFX=	.tar.Z
+
+MAINTAINER=	tonym@biolateral.com.au
+
+BUILD_DEPENDS=	${LOCALBASE}/lib/ncbi/libncbi.a:${PORTSDIR}/biology/ncbi-toolkit
+
+do-install:
+	@${MKDIR} ${PREFIX}/bin
+	@${INSTALL_PROGRAM} ${WRKSRC}/nclever ${PREFIX}/bin
+.if !defined(NOPORTSDOCS)
+	@${MKDIR} ${DOCSDIR}
+	@${INSTALL_DATA} ${WRKSRC}/nclever_manual.txt ${DOCSDIR}
+	@${INSTALL_DATA} ${WRKSRC}/nclever.citation ${DOCSDIR}
+	@${INSTALL_DATA} ${WRKSRC}/sample_script1.txt ${DOCSDIR}
+	@${INSTALL_DATA} ${WRKSRC}/sample_script2.txt ${DOCSDIR}
+.endif
+
+.include <bsd.port.mk>
diff --git a/biology/nclever/distinfo b/biology/nclever/distinfo
new file mode 100644
index 000000000000..792fa5ef5069
--- /dev/null
+++ b/biology/nclever/distinfo
@@ -0,0 +1 @@
+MD5 (nclever4.0.tar.Z) = ef1c97fe8769b41e0fa8773848d70836
diff --git a/biology/nclever/files/patch-main b/biology/nclever/files/patch-main
new file mode 100644
index 000000000000..0014e55b9ef8
--- /dev/null
+++ b/biology/nclever/files/patch-main
@@ -0,0 +1,11 @@
+--- main.c.orig	Mon Sep 24 16:34:16 2001
++++ main.c	Mon Sep 24 16:37:26 2001
+@@ -358,7 +358,7 @@
+ /* Read a line from stdin */
+ static Boolean GetCommand(void)
+ {
+-    if (!gets(Command)) return(FALSE);
++    if (!fgets(Command,MAXLINELEN-1,stdin)) return(FALSE);
+     if (EchoCommands) fprintf(CmdStream,"%s\n",Command);
+     return(TRUE);
+ }
diff --git a/biology/nclever/files/patch-makefile b/biology/nclever/files/patch-makefile
new file mode 100644
index 000000000000..1a97f20d9bd3
--- /dev/null
+++ b/biology/nclever/files/patch-makefile
@@ -0,0 +1,47 @@
+--- Makefile.orig	Thu Dec  7 11:11:31 2000
++++ Makefile	Thu Dec  7 11:34:11 2000
+@@ -29,7 +29,8 @@
+ # NCBI librairies are needed.
+ 
+ # Set the correct path to the NCBI package
+-NCBI    = /usr/local/lib/NCBI
++NCBILIB = /usr/local/lib/ncbi
++NCBIINC = /usr/local/include/ncbi
+ 
+ # Set the name of your ANSI C compiler
+ CC      = gcc
+@@ -39,7 +40,7 @@
+ LIBSNCBI  = -lncbiNacc -lnetentr -lncbicdr -lncbiobj -lnetcli -lncbi
+ # System linking libraries (these are used under Solaris 2.6;
+ # adjust according to your site).
+-LIBSSYS   = -lm -lsocket -lnsl -lxnet
++LIBSSYS   = -lm
+ 
+ #
+ # Nothing to adjust below this line !
+@@ -50,20 +51,20 @@
+ all: nclever
+ 
+ nclever: $(OBJS)
+-	$(CC) $(CCFLAGS) -o nclever -L$(NCBI)/lib $(OBJS) $(LIBSNCBI) $(LIBSSYS)
++	$(CC) $(CCFLAGS) -o nclever -L$(NCBILIB) $(OBJS) $(LIBSNCBI) $(LIBSSYS)
+ 	strip nclever
+ 
+ main.o: main.c main.h
+-	$(CC) $(CCFLAGS) -c -I$(NCBI)/include main.c
++	$(CC) $(CCFLAGS) -c -I$(NCBIINC) main.c
+ 
+ lists.o: lists.c main.h
+-	$(CC) $(CCFLAGS) -c -I$(NCBI)/include lists.c
++	$(CC) $(CCFLAGS) -c -I$(NCBIINC) lists.c
+ 
+ print.o: print.c main.h
+-	$(CC) $(CCFLAGS) -c -I$(NCBI)/include print.c
++	$(CC) $(CCFLAGS) -c -I$(NCBIINC) print.c
+ 
+ entinfo.o: entinfo.c main.h
+-	$(CC) $(CCFLAGS) -c -I$(NCBI)/include entinfo.c
++	$(CC) $(CCFLAGS) -c -I$(NCBIINC) entinfo.c
+ 
+ clean:
+ 	rm *.o
diff --git a/biology/nclever/pkg-comment b/biology/nclever/pkg-comment
new file mode 100644
index 000000000000..bcc0475ce55a
--- /dev/null
+++ b/biology/nclever/pkg-comment
@@ -0,0 +1 @@
+NClever is a character-based version of NCBI's Entrez program
diff --git a/biology/nclever/pkg-descr b/biology/nclever/pkg-descr
new file mode 100644
index 000000000000..88fe809475c6
--- /dev/null
+++ b/biology/nclever/pkg-descr
@@ -0,0 +1,8 @@
+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
+
+--
+Tony Maher <tonym@biolateral.com.au>
diff --git a/biology/nclever/pkg-plist b/biology/nclever/pkg-plist
new file mode 100644
index 000000000000..c722d162e7c5
--- /dev/null
+++ b/biology/nclever/pkg-plist
@@ -0,0 +1,6 @@
+bin/nclever
+%%PORTDOCS%%share/doc/nclever/nclever.citation
+%%PORTDOCS%%share/doc/nclever/nclever_manual.txt
+%%PORTDOCS%%share/doc/nclever/sample_script1.txt
+%%PORTDOCS%%share/doc/nclever/sample_script2.txt
+%%PORTDOCS%%@dirrm share/doc/nclever