From 0149bce295e707f5b9641b1c32d084824a6be0e3 Mon Sep 17 00:00:00 2001
From: Pav Lucistnik <pav@FreeBSD.org>
Date: Wed, 14 May 2008 14:07:01 +0000
Subject: NJplot is a tree drawing program able to draw any phylogenetic tree
expressed in the Newick phylogenetic tree format (e.g., the format used by
the PHYLIP package). NJplot is especially convenient for rooting the unrooted
trees obtained from parsimony, distance or maximum likelihood tree-building
methods.
The package contains the following programs:
njplot - draw phylogenetic trees and interactively modify them
newicktops - non-interactive version rendering into a PostScript file
newicktotxt - non-interactive version rendering into a text file
unrooted - draw unrooted circular trees
If you use NJplot in a published work, please cite the following reference:
Perriere, G. and Gouy, M. (1996) WWW-Query: An on-line retrieval system for
biological sequence banks. Biochimie, 78, 364-369.
WWW: http://pbil.univ-lyon1.fr/software/njplot.html
PR: ports/118438
Submitted by: Motomichi Matsuzaki <mzaki@biol.s.u-tokyo.ac.jp>
---
biology/njplot/Makefile | 55 +++++++++++++++++++++++++++++
biology/njplot/distinfo | 3 ++
biology/njplot/files/patch-makefile | 69 +++++++++++++++++++++++++++++++++++++
biology/njplot/pkg-descr | 17 +++++++++
4 files changed, 144 insertions(+)
create mode 100644 biology/njplot/Makefile
create mode 100644 biology/njplot/distinfo
create mode 100644 biology/njplot/files/patch-makefile
create mode 100644 biology/njplot/pkg-descr
(limited to 'biology/njplot')
diff --git a/biology/njplot/Makefile b/biology/njplot/Makefile
new file mode 100644
index 000000000000..9e118db518cb
--- /dev/null
+++ b/biology/njplot/Makefile
@@ -0,0 +1,55 @@
+# New ports collection makefile for: njplot
+# Date created: 5 December 2007
+# Whom: Motomichi Matsuzaki <mzaki@biol.s.u-tokyo.ac.jp>
+#
+# $FreeBSD$
+#
+
+PORTNAME= njplot
+PORTVERSION= 2.1
+CATEGORIES= biology
+MASTER_SITES= ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/njplot/archive/
+
+MAINTAINER= mzaki@biol.s.u-tokyo.ac.jp
+COMMENT= Phylogenetic tree drawing program capable of interactive manipulation
+
+.ifndef (WITHOUT_X11)
+BUILD_DEPENDS= ${LOCALBASE}/lib/ncbi/libvibrant.a:${PORTSDIR}/biology/ncbi-toolkit
+USE_XLIB= yes
+USE_MOTIF= yes
+.endif
+
+MAKEFILE= makefile
+
+BINARIES= newicktops newicktotxt
+.ifndef (WITHOUT_X11)
+BINARIES+= njplot unrooted
+.endif
+.for file in ${BINARIES}
+PLIST_FILES+= bin/${file}
+.endfor
+
+PORTDOCS= njplot.help njplot.html njplot.gif
+
+MAN1= njplot.1 unrooted.1
+
+.ifdef (WITHOUT_X11)
+post-patch:
+ ${REINPLACE_CMD} -e 's|njplot.*unrooted||' ${WRKSRC}/makefile
+.endif
+
+do-install:
+.for file in ${BINARIES}
+ ${INSTALL_PROGRAM} ${WRKSRC}/${file} ${PREFIX}/bin
+.endfor
+.for file in ${MAN1}
+ ${INSTALL_MAN} ${WRKSRC}/${file} ${PREFIX}/man/man1
+.endfor
+.if !defined(NOPORTDOCS)
+ ${MKDIR} ${DOCSDIR}
+.for file in ${PORTDOCS}
+ ${INSTALL_MAN} ${WRKSRC}/${file} ${DOCSDIR}
+.endfor
+.endif
+
+.include <bsd.port.mk>
diff --git a/biology/njplot/distinfo b/biology/njplot/distinfo
new file mode 100644
index 000000000000..74d09b4c0b59
--- /dev/null
+++ b/biology/njplot/distinfo
@@ -0,0 +1,3 @@
+MD5 (njplot-2.1.tar.gz) = d98adc1e624e8fcc8cc86e7dfe65e67c
+SHA256 (njplot-2.1.tar.gz) = dd8a54c3903cd104d8322257a87b5fbf3afb7776a96fcf9bee504ae1ad54c0c1
+SIZE (njplot-2.1.tar.gz) = 85735
diff --git a/biology/njplot/files/patch-makefile b/biology/njplot/files/patch-makefile
new file mode 100644
index 000000000000..448fbe7d41be
--- /dev/null
+++ b/biology/njplot/files/patch-makefile
@@ -0,0 +1,69 @@
+--- makefile.orig Thu Oct 11 01:54:00 2007
++++ makefile Mon Dec 3 22:08:28 2007
+@@ -1,5 +1,5 @@
+ #uncomment and locally adapt next line to fix the full helpfile path name
+-HELPFILENAME = -DHELPFILENAME=\"/usr/share/njplot/njplot.help\"
++HELPFILENAME = -DHELPFILENAME=\"$(LOCALBASE)/doc/njplot/njplot.help\"
+
+ #comment out next line and uncomment next 2 to use the PDFLib Lite library
+ NO_PDF = -DNO_PDF
+@@ -7,43 +7,45 @@
+ #PDFLIB = -L$(PDF) -lpdf
+
+ # c compiler and linker
+-CC = gcc
++CC ?= gcc
+
+ # Vibrant top directory
+-VIBRANT = /banques0/ncbiJun04
++#VIBRANT = /banques0/ncbiJun04
++NCBIINC = $(LOCALBASE)/include/ncbi
++NCBILIB = $(LOCALBASE)/lib/ncbi
+
+
+ # X11 include directory
+-X11INCL = /usr/X11R6/include
++X11INCL = $(LOCALBASE)/include
+
+ # motif library directory
+-MOTIFLIB = /sw/lib
+-MOTIFINCL = /sw/include
++#MOTIFLIB = /sw/lib
++#MOTIFINCL = /sw/include
+
+ OBJECTS = njplot-vib.o
+ OBJUNROOTED = unrooted-vib.o preptree.o
+
+
+-CFLAGS = -c -DWIN_MOTIF -Dunix -I$(VIBRANT)/include -I$(VIBRANT)/vibrant -I$(VIBRANT)/corelib \
+- -I$(VIBRANT) -I$(PDF) -I$(X11INCL) -I$(MOTIFINCL) $(HELPFILENAME) $(NO_PDF) \
+- -Wimplicit-function-declaration -g
++CFLAGS = -c -DWIN_MOTIF -Dunix -I$(NCBIINC) \
++ -I$(X11INCL) $(HELPFILENAME) $(NO_PDF) \
++ -Wimplicit-function-declaration
+
+ all: njplot unrooted newicktops newicktotxt
+
+
+ njplot : $(OBJECTS)
+ $(CC) -g -o njplot $(OBJECTS) \
+- -L$(VIBRANT)/lib \
++ -L$(NCBILIB) \
+ -lvibrant -lncbi \
+ $(PDFLIB) \
+- -L$(MOTIFLIB) -lXm \
+- -L/usr/X11R6/lib -lXmu -lXt -lX11 -lm
++ $(MOTIFLIB) \
++ -L$(X11BASE)/lib -lXmu -lXt -lX11 -lm
+
+ unrooted : $(OBJUNROOTED)
+ $(CC) -g -o unrooted $(OBJUNROOTED) \
+- -L$(VIBRANT)/lib -lvibrant -lncbi \
+- -L$(MOTIFLIB) -lXm \
+- -L/usr/X11R6/lib -lXmu -lXt -lX11 -lm
++ -L$(NCBILIB) -lvibrant -lncbi \
++ $(MOTIFLIB) \
++ -L$(LOCALBASE)/lib -lXmu -lXt -lX11 -lm
+
+ newicktops: njplot-vib.c
+ $(CC) -DNO_GUI -DNO_PDF -o $@ njplot-vib.c -lm
diff --git a/biology/njplot/pkg-descr b/biology/njplot/pkg-descr
new file mode 100644
index 000000000000..679993f19121
--- /dev/null
+++ b/biology/njplot/pkg-descr
@@ -0,0 +1,17 @@
+NJplot is a tree drawing program able to draw any phylogenetic tree expressed
+in the Newick phylogenetic tree format (e.g., the format used by the PHYLIP
+package). NJplot is especially convenient for rooting the unrooted trees
+obtained from parsimony, distance or maximum likelihood tree-building methods.
+
+The package contains the following programs:
+njplot - draw phylogenetic trees and interactively modify them
+newicktops - non-interactive version rendering into a PostScript file
+newicktotxt - non-interactive version rendering into a text file
+unrooted - draw unrooted circular trees
+
+If you use NJplot in a published work, please cite the following reference:
+
+Perriere, G. and Gouy, M. (1996) WWW-Query: An on-line retrieval system for
+biological sequence banks. Biochimie, 78, 364-369.
+
+WWW: http://pbil.univ-lyon1.fr/software/njplot.html
--
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